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Molybdenum in PDB 2afi: Crystal Structure of Mgadp Bound AV2-AV1 Complex

Enzymatic activity of Crystal Structure of Mgadp Bound AV2-AV1 Complex

All present enzymatic activity of Crystal Structure of Mgadp Bound AV2-AV1 Complex:
1.18.6.1;

Protein crystallography data

The structure of Crystal Structure of Mgadp Bound AV2-AV1 Complex, PDB code: 2afi was solved by F.A.Tezcan, J.T.Kaiser, D.Mustafi, M.Y.Walton, J.B.Howard, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.43 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 72.915, 141.432, 165.549, 73.69, 79.37, 76.58
R / Rfree (%) 22.9 / 27

Other elements in 2afi:

The structure of Crystal Structure of Mgadp Bound AV2-AV1 Complex also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Iron (Fe) 76 atoms
Calcium (Ca) 4 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Crystal Structure of Mgadp Bound AV2-AV1 Complex (pdb code 2afi). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 4 binding sites of Molybdenum where determined in the Crystal Structure of Mgadp Bound AV2-AV1 Complex, PDB code: 2afi:
Jump to Molybdenum binding site number: 1; 2; 3; 4;

Molybdenum binding site 1 out of 4 in 2afi

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Molybdenum binding site 1 out of 4 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


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 Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo496

b:19.2
occ:1.00
MO1 A:CFN496 0.0 19.2 1.0
O5 A:HCA494 2.1 22.9 1.0
O7 A:HCA494 2.2 21.2 1.0
ND1 A:HIS442 2.3 19.1 1.0
S3B A:CFN496 2.3 17.9 1.0
S4B A:CFN496 2.3 16.7 1.0
S1B A:CFN496 2.4 19.4 1.0
FE7 A:CFN496 2.7 14.5 1.0
FE5 A:CFN496 2.7 19.6 1.0
FE6 A:CFN496 2.8 15.9 1.0
C7 A:HCA494 2.9 24.3 1.0
C3 A:HCA494 3.0 24.0 1.0
CE1 A:HIS442 3.1 18.8 1.0
CG A:HIS442 3.4 22.1 1.0
NX A:CFN496 3.6 19.8 1.0
CB A:HIS442 3.8 23.3 1.0
C2 A:HCA494 3.9 25.1 1.0
O6 A:HCA494 4.1 25.5 1.0
C4 A:HCA494 4.2 26.9 1.0
C5 A:HCA494 4.2 27.8 1.0
NE2 A:HIS442 4.2 22.4 1.0
O2 A:HCA494 4.3 30.8 1.0
CD2 A:HIS442 4.4 21.2 1.0
CA A:HIS442 4.5 23.6 1.0
C1 A:HCA494 4.7 29.5 1.0
S5A A:CFN496 4.8 15.0 1.0
S3A A:CFN496 4.9 28.1 1.0
S2B A:CFN496 4.9 23.6 1.0
FE3 A:CFN496 5.0 21.0 1.0

Molybdenum binding site 2 out of 4 in 2afi

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Molybdenum binding site 2 out of 4 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


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 Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo496

b:14.9
occ:1.00
MO1 C:CFN496 0.0 14.9 1.0
O5 C:HCA494 2.2 18.6 1.0
O7 C:HCA494 2.2 18.7 1.0
S1B C:CFN496 2.3 9.1 1.0
ND1 C:HIS442 2.3 9.6 1.0
S3B C:CFN496 2.3 14.0 1.0
S4B C:CFN496 2.4 16.4 1.0
FE6 C:CFN496 2.7 12.5 1.0
FE5 C:CFN496 2.7 13.4 1.0
FE7 C:CFN496 2.8 13.7 1.0
C7 C:HCA494 2.9 18.6 1.0
C3 C:HCA494 3.0 19.2 1.0
CE1 C:HIS442 3.0 14.6 1.0
CG C:HIS442 3.4 12.9 1.0
NX C:CFN496 3.6 15.8 1.0
C2 C:HCA494 3.8 22.9 1.0
CB C:HIS442 3.9 16.7 1.0
O6 C:HCA494 4.1 19.2 1.0
C5 C:HCA494 4.2 25.1 1.0
C4 C:HCA494 4.2 18.7 1.0
O2 C:HCA494 4.2 27.2 1.0
NE2 C:HIS442 4.2 17.4 1.0
CD2 C:HIS442 4.4 16.8 1.0
C1 C:HCA494 4.5 25.2 1.0
CA C:HIS442 4.7 22.2 1.0
S2B C:CFN496 4.8 18.5 1.0
S3A C:CFN496 4.8 18.5 1.0
S5A C:CFN496 4.9 17.6 1.0

Molybdenum binding site 3 out of 4 in 2afi

Go back to Molybdenum Binding Sites List in 2afi
Molybdenum binding site 3 out of 4 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


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 Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mo496

b:24.6
occ:1.00
MO1 I:CFN496 0.0 24.6 1.0
O5 I:HCA494 2.1 27.8 1.0
O7 I:HCA494 2.2 22.4 1.0
ND1 I:HIS442 2.3 16.2 1.0
S3B I:CFN496 2.3 17.9 1.0
S4B I:CFN496 2.3 22.0 1.0
S1B I:CFN496 2.3 20.8 1.0
FE7 I:CFN496 2.7 18.6 1.0
FE6 I:CFN496 2.7 18.6 1.0
FE5 I:CFN496 2.7 24.5 1.0
C7 I:HCA494 2.9 24.3 1.0
CE1 I:HIS442 3.0 18.7 1.0
C3 I:HCA494 3.1 21.3 1.0
CG I:HIS442 3.4 19.4 1.0
NX I:CFN496 3.5 20.8 1.0
CB I:HIS442 3.8 20.6 1.0
C2 I:HCA494 3.9 25.8 1.0
O6 I:HCA494 4.1 32.2 1.0
C5 I:HCA494 4.2 26.0 1.0
C4 I:HCA494 4.2 19.6 1.0
NE2 I:HIS442 4.2 23.2 1.0
O2 I:HCA494 4.3 37.2 1.0
CD2 I:HIS442 4.4 22.5 1.0
CA I:HIS442 4.6 22.6 1.0
C1 I:HCA494 4.7 32.6 1.0
S3A I:CFN496 4.8 27.9 1.0
S5A I:CFN496 4.8 23.3 1.0
S2B I:CFN496 4.9 24.7 1.0
FE4 I:CFN496 5.0 18.5 1.0
FE3 I:CFN496 5.0 25.8 1.0

Molybdenum binding site 4 out of 4 in 2afi

Go back to Molybdenum Binding Sites List in 2afi
Molybdenum binding site 4 out of 4 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Crystal Structure of Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mo496

b:22.9
occ:1.00
MO1 K:CFN496 0.0 22.9 1.0
O5 K:HCA494 2.2 21.6 1.0
O7 K:HCA494 2.2 17.5 1.0
S3B K:CFN496 2.3 26.2 1.0
S4B K:CFN496 2.3 19.2 1.0
ND1 K:HIS442 2.3 21.2 1.0
S1B K:CFN496 2.3 21.4 1.0
FE7 K:CFN496 2.7 16.5 1.0
FE5 K:CFN496 2.7 19.3 1.0
FE6 K:CFN496 2.7 23.3 1.0
C7 K:HCA494 2.9 21.2 1.0
C3 K:HCA494 3.0 21.2 1.0
CE1 K:HIS442 3.1 20.1 1.0
CG K:HIS442 3.4 21.7 1.0
NX K:CFN496 3.6 20.2 1.0
CB K:HIS442 3.9 20.1 1.0
C2 K:HCA494 3.9 22.6 1.0
O6 K:HCA494 4.1 23.4 1.0
C5 K:HCA494 4.2 30.8 1.0
C4 K:HCA494 4.2 22.9 1.0
NE2 K:HIS442 4.2 20.2 1.0
O2 K:HCA494 4.2 29.6 1.0
CD2 K:HIS442 4.4 22.6 1.0
CA K:HIS442 4.6 20.9 1.0
C1 K:HCA494 4.6 26.6 1.0
S5A K:CFN496 4.8 25.2 1.0
S3A K:CFN496 4.8 25.4 1.0
S2B K:CFN496 4.9 22.2 1.0

Reference:

F.A.Tezcan, J.T.Kaiser, D.Mustafi, M.Y.Walton, J.B.Howard, D.C.Rees. Nitrogenase Complexes: Multiple Docking Sites For A Nucleotide Switch Protein Science V. 309 1377 2005.
ISSN: ISSN 0036-8075
PubMed: 16123301
DOI: 10.1126/SCIENCE.1115653
Page generated: Tue Dec 15 05:16:57 2020

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