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Molybdenum in PDB 4ydd: Crystal Structure of the Perchlorate Reductase Pcrab From Azospira Suillum Ps

Protein crystallography data

The structure of Crystal Structure of the Perchlorate Reductase Pcrab From Azospira Suillum Ps, PDB code: 4ydd was solved by C.-L.Tsai, M.D.Youngblut, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.35 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 132.827, 175.501, 193.160, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23.7

Other elements in 4ydd:

The structure of Crystal Structure of the Perchlorate Reductase Pcrab From Azospira Suillum Ps also contains other interesting chemical elements:

Iron (Fe) 57 atoms
Sodium (Na) 1 atom

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Crystal Structure of the Perchlorate Reductase Pcrab From Azospira Suillum Ps (pdb code 4ydd). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 3 binding sites of Molybdenum where determined in the Crystal Structure of the Perchlorate Reductase Pcrab From Azospira Suillum Ps, PDB code: 4ydd:
Jump to Molybdenum binding site number: 1; 2; 3;

Molybdenum binding site 1 out of 3 in 4ydd

Go back to Molybdenum Binding Sites List in 4ydd
Molybdenum binding site 1 out of 3 in the Crystal Structure of the Perchlorate Reductase Pcrab From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Crystal Structure of the Perchlorate Reductase Pcrab From Azospira Suillum Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1002

b:20.9
occ:1.00
H13 A:MGD1003 1.4 20.5 1.0
OD2 A:ASP170 2.0 19.9 1.0
H12 A:MD11004 2.1 23.0 1.0
H12 A:MGD1003 2.2 23.4 1.0
S13 A:MD11004 2.2 18.4 1.0
S13 A:MGD1003 2.4 17.1 1.0
S12 A:MD11004 2.4 19.1 1.0
O A:HOH1110 2.5 21.3 1.0
S12 A:MGD1003 2.6 19.5 1.0
CG A:ASP170 2.8 22.4 1.0
H13 A:MD11004 3.0 22.0 1.0
OD1 A:ASP170 3.0 21.4 1.0
C13 A:MD11004 3.3 18.7 1.0
HA3 A:GLY459 3.3 23.1 1.0
C12 A:MD11004 3.4 18.3 1.0
HE1 A:HIS770 3.4 20.2 1.0
C13 A:MGD1003 3.5 16.7 1.0
HE1 A:HIS764 3.6 20.2 1.0
C12 A:MGD1003 3.6 17.9 1.0
HB3 A:TYR168 3.7 25.5 1.0
H A:GLY459 3.9 24.5 1.0
HB A:ILE458 3.9 24.0 1.0
N A:GLY459 3.9 20.4 1.0
HD21 A:ASN35 3.9 20.1 1.0
CA A:GLY459 3.9 19.3 1.0
HA2 A:GLY459 4.0 23.1 1.0
HD2 A:TYR168 4.2 25.8 1.0
CE1 A:HIS770 4.2 16.9 1.0
CB A:ASP170 4.3 23.5 1.0
HE2 A:HIS770 4.4 20.4 1.0
C A:ILE458 4.4 18.6 1.0
CB A:TYR168 4.5 21.3 1.0
CE1 A:HIS764 4.5 16.9 1.0
HE2 A:HIS426 4.5 24.4 1.0
ND2 A:ASN35 4.5 16.7 1.0
HB2 A:TYR168 4.6 25.5 1.0
HB2 A:ASP170 4.6 28.2 1.0
HB3 A:ASP170 4.6 28.2 1.0
CD2 A:TYR168 4.6 21.5 1.0
NE2 A:HIS770 4.6 17.0 1.0
C14 A:MD11004 4.7 17.3 1.0
HE1 A:HIS426 4.7 22.7 1.0
CB A:ILE458 4.7 20.0 1.0
HG22 A:ILE458 4.7 24.0 1.0
H14 A:MD11004 4.7 20.8 1.0
CG A:TYR168 4.8 21.1 1.0
HD22 A:ASN35 4.8 20.1 1.0
C14 A:MGD1003 4.8 17.3 1.0
H15 A:MD11004 4.8 18.2 1.0
C11 A:MD11004 4.9 17.6 1.0
O A:ILE458 4.9 18.9 1.0
H15 A:MGD1003 4.9 20.1 1.0
C11 A:MGD1003 4.9 16.6 1.0

Molybdenum binding site 2 out of 3 in 4ydd

Go back to Molybdenum Binding Sites List in 4ydd
Molybdenum binding site 2 out of 3 in the Crystal Structure of the Perchlorate Reductase Pcrab From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Crystal Structure of the Perchlorate Reductase Pcrab From Azospira Suillum Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo1002

b:24.4
occ:1.00
H13 C:MGD1003 1.3 27.0 1.0
H12 C:MD11004 1.7 24.2 1.0
OD2 C:ASP170 2.0 26.8 1.0
H12 C:MGD1003 2.1 30.0 1.0
S13 C:MGD1003 2.3 22.5 1.0
S13 C:MD11004 2.3 21.0 1.0
S12 C:MD11004 2.4 20.1 1.0
S12 C:MGD1003 2.6 25.0 1.0
CG C:ASP170 2.9 28.0 1.0
O C:HOH1317 2.9 30.7 1.0
H13 C:MD11004 2.9 25.2 1.0
OD1 C:ASP170 3.2 24.8 1.0
C13 C:MD11004 3.4 21.9 1.0
HA3 C:GLY459 3.4 32.3 1.0
C12 C:MD11004 3.4 21.3 1.0
C13 C:MGD1003 3.4 23.1 1.0
HE1 C:HIS770 3.5 25.7 1.0
HE1 C:HIS764 3.5 25.6 1.0
C12 C:MGD1003 3.5 23.2 1.0
HB3 C:TYR168 3.6 26.2 1.0
N C:GLY459 3.9 26.4 1.0
CA C:GLY459 3.9 26.9 1.0
H C:GLY459 3.9 31.7 1.0
HD21 C:ASN35 4.0 28.0 1.0
HA2 C:GLY459 4.0 32.3 1.0
HB C:ILE458 4.0 31.9 1.0
HD2 C:TYR168 4.1 26.4 1.0
CE1 C:HIS770 4.2 21.4 1.0
O C:HOH1429 4.2 29.6 1.0
CB C:ASP170 4.3 28.1 1.0
HE2 C:HIS770 4.3 25.6 1.0
C C:ILE458 4.3 25.6 1.0
CE1 C:HIS764 4.4 21.3 1.0
CB C:TYR168 4.4 21.9 1.0
HB3 C:ASP170 4.5 33.7 1.0
HB2 C:TYR168 4.5 26.2 1.0
HB2 C:ASP170 4.5 33.7 1.0
HE2 C:HIS426 4.5 27.3 1.0
CD2 C:TYR168 4.6 22.0 1.0
ND2 C:ASN35 4.6 23.3 1.0
NE2 C:HIS770 4.6 21.4 1.0
HG22 C:ILE458 4.7 33.5 1.0
C14 C:MD11004 4.7 20.9 1.0
HE1 C:HIS426 4.7 26.0 1.0
C14 C:MGD1003 4.8 22.6 1.0
CG C:TYR168 4.8 22.1 1.0
O C:ILE458 4.8 26.1 1.0
CB C:ILE458 4.8 26.6 1.0
H14 C:MD11004 4.8 25.0 1.0
C11 C:MGD1003 4.9 23.1 1.0
C11 C:MD11004 4.9 19.4 1.0
HD22 C:ASN35 4.9 28.0 1.0
H102 C:MD11004 4.9 22.9 1.0
H15 C:MGD1003 4.9 25.1 1.0
HA C:ILE458 5.0 31.4 1.0
CA C:ILE458 5.0 26.2 1.0
H14 C:MGD1003 5.0 27.2 1.0

Molybdenum binding site 3 out of 3 in 4ydd

Go back to Molybdenum Binding Sites List in 4ydd
Molybdenum binding site 3 out of 3 in the Crystal Structure of the Perchlorate Reductase Pcrab From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Crystal Structure of the Perchlorate Reductase Pcrab From Azospira Suillum Ps within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mo1002

b:22.0
occ:1.00
H12 E:MD11004 1.8 22.8 1.0
H12 E:MGD1003 2.0 30.8 1.0
H13 E:MD11004 2.0 23.1 1.0
OD2 E:ASP170 2.1 24.1 1.0
S13 E:MD11004 2.3 19.3 1.0
S12 E:MD11004 2.4 19.0 1.0
S13 E:MGD1003 2.4 20.0 1.0
S12 E:MGD1003 2.5 25.7 1.0
CG E:ASP170 2.9 25.6 1.0
H13 E:MGD1003 3.2 24.0 1.0
OD1 E:ASP170 3.2 24.6 1.0
C13 E:MD11004 3.3 19.3 1.0
O E:HOH1399 3.3 27.1 1.0
HA3 E:GLY459 3.4 25.8 1.0
C12 E:MD11004 3.4 18.7 1.0
HE1 E:HIS770 3.5 21.5 1.0
C13 E:MGD1003 3.5 19.6 1.0
HE1 E:HIS764 3.6 23.5 1.0
HB3 E:TYR168 3.6 25.5 1.0
C12 E:MGD1003 3.6 20.4 1.0
H E:GLY459 3.9 26.5 1.0
HD21 E:ASN35 3.9 25.2 1.0
HB E:ILE458 3.9 29.3 1.0
N E:GLY459 3.9 22.1 1.0
CA E:GLY459 4.0 21.5 1.0
HA2 E:GLY459 4.1 25.8 1.0
HD2 E:TYR168 4.1 25.9 1.0
CE1 E:HIS770 4.2 17.9 1.0
CB E:ASP170 4.4 26.7 1.0
HE2 E:HIS770 4.4 20.4 1.0
CB E:TYR168 4.4 21.2 1.0
CE1 E:HIS764 4.4 19.6 1.0
HB2 E:TYR168 4.5 25.5 1.0
C E:ILE458 4.5 22.1 1.0
ND2 E:ASN35 4.5 21.0 1.0
HE2 E:HIS426 4.6 27.5 1.0
CD2 E:TYR168 4.6 21.6 1.0
HG22 E:ILE458 4.6 28.6 1.0
HB2 E:ASP170 4.6 32.0 1.0
HB3 E:ASP170 4.6 32.0 1.0
NE2 E:HIS770 4.7 17.0 1.0
C14 E:MD11004 4.7 18.8 1.0
HD22 E:ASN35 4.8 25.2 1.0
CB E:ILE458 4.8 24.4 1.0
HE1 E:HIS426 4.8 24.8 1.0
CG E:TYR168 4.8 21.0 1.0
H14 E:MD11004 4.8 22.6 1.0
C14 E:MGD1003 4.8 19.8 1.0
C11 E:MD11004 4.8 17.6 1.0
H15 E:MGD1003 4.9 22.3 1.0
C11 E:MGD1003 4.9 19.9 1.0
H15 E:MD11004 5.0 21.7 1.0
O E:ILE458 5.0 21.6 1.0

Reference:

M.D.Youngblut, C.L.Tsai, I.C.Clark, H.K.Carlson, A.P.Maglaqui, P.S.Gau-Pan, S.A.Redford, A.Wong, J.A.Tainer, J.D.Coates. Perchlorate Reductase Is Distinguished By Active Site Aromatic Gate Residues. J.Biol.Chem. V. 291 9190 2016.
ISSN: ESSN 1083-351X
PubMed: 26940877
DOI: 10.1074/JBC.M116.714618
Page generated: Tue Dec 15 05:19:31 2020

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