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Molybdenum in PDB 6bbl: Crystal Structure of the A-96GLN Mofe Protein Variant in the Presence of the Substrate Acetylene

Enzymatic activity of Crystal Structure of the A-96GLN Mofe Protein Variant in the Presence of the Substrate Acetylene

All present enzymatic activity of Crystal Structure of the A-96GLN Mofe Protein Variant in the Presence of the Substrate Acetylene:
1.18.6.1;

Protein crystallography data

The structure of Crystal Structure of the A-96GLN Mofe Protein Variant in the Presence of the Substrate Acetylene, PDB code: 6bbl was solved by O.A.Zadvornyy, S.M.Keable, J.Vertemara, B.J.Eilers, D.Karamatullah, A.J.Rasmussen, L.De Gioia, G.Zampella, L.C.Seefeldt, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.76 / 1.68
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.781, 128.251, 107.272, 90.00, 109.11, 90.00
R / Rfree (%) 15.1 / 18.5

Other elements in 6bbl:

The structure of Crystal Structure of the A-96GLN Mofe Protein Variant in the Presence of the Substrate Acetylene also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 32 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Crystal Structure of the A-96GLN Mofe Protein Variant in the Presence of the Substrate Acetylene (pdb code 6bbl). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Crystal Structure of the A-96GLN Mofe Protein Variant in the Presence of the Substrate Acetylene, PDB code: 6bbl:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in 6bbl

Go back to Molybdenum Binding Sites List in 6bbl
Molybdenum binding site 1 out of 2 in the Crystal Structure of the A-96GLN Mofe Protein Variant in the Presence of the Substrate Acetylene


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 A-96GLN Mofe Protein Variant in the Presence of the Substrate Acetylene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo504

b:19.0
occ:1.00
MO1 A:ICS504 0.0 19.0 1.0
S3B A:ICS504 2.2 16.9 1.0
O7 A:HCA503 2.2 19.4 1.0
S4B A:ICS504 2.2 16.4 0.9
S1B A:ICS504 2.3 17.2 1.0
O6 A:HCA503 2.3 19.0 1.0
ND1 A:HIS442 2.5 22.8 1.0
FE6 A:ICS504 2.7 17.6 1.0
FE7 A:ICS504 2.7 17.3 1.0
FE5 A:ICS504 2.7 17.6 1.0
C7 A:HCA503 3.0 21.4 1.0
HB3 A:HIS442 3.0 23.0 1.0
C3 A:HCA503 3.1 22.7 1.0
CE1 A:HIS442 3.4 20.1 1.0
CG A:HIS442 3.5 15.6 1.0
HE1 A:HIS442 3.5 24.1 1.0
CX A:ICS504 3.6 10.6 1.0
H52 A:HCA503 3.7 27.5 1.0
CB A:HIS442 3.7 19.2 1.0
H22 A:HCA503 4.1 24.1 1.0
C2 A:HCA503 4.1 20.1 1.0
C4 A:HCA503 4.2 20.6 1.0
O A:HOH811 4.2 20.1 1.0
O2 A:HCA503 4.2 23.3 1.0
HA A:HIS442 4.2 19.8 1.0
O5 A:HCA503 4.3 19.0 1.0
HB2 A:HIS442 4.4 23.0 1.0
H41 A:HCA503 4.4 24.7 1.0
C5 A:HCA503 4.4 22.9 1.0
NE2 A:HIS442 4.5 20.3 1.0
HG22 A:ILE355 4.5 23.4 1.0
CA A:HIS442 4.6 16.5 1.0
CD2 A:HIS442 4.6 15.8 1.0
C1 A:HCA503 4.7 22.4 1.0
S2B A:ICS504 4.8 18.2 1.0
S5A A:ICS504 4.8 19.6 1.0
HA3 A:GLY356 4.9 22.1 1.0
S3A A:ICS504 4.9 17.6 1.0
FE2 A:ICS504 5.0 17.1 1.0
FE3 A:ICS504 5.0 17.0 1.0
H51 A:HCA503 5.0 27.5 1.0
FE4 A:ICS504 5.0 17.9 1.0

Molybdenum binding site 2 out of 2 in 6bbl

Go back to Molybdenum Binding Sites List in 6bbl
Molybdenum binding site 2 out of 2 in the Crystal Structure of the A-96GLN Mofe Protein Variant in the Presence of the Substrate Acetylene


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 A-96GLN Mofe Protein Variant in the Presence of the Substrate Acetylene within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo503

b:18.8
occ:1.00
MO1 C:ICS503 0.0 18.8 1.0
O7 C:HCA502 2.2 16.5 1.0
S3B C:ICS503 2.2 18.2 1.0
O5 C:HCA502 2.2 19.0 1.0
S1B C:ICS503 2.3 17.6 1.0
S4B C:ICS503 2.3 17.6 1.0
ND1 C:HIS442 2.4 16.7 1.0
FE6 C:ICS503 2.7 17.2 1.0
FE7 C:ICS503 2.7 17.8 1.0
FE5 C:ICS503 2.7 17.4 1.0
C7 C:HCA502 3.0 20.6 1.0
HB3 C:HIS442 3.0 20.2 1.0
C3 C:HCA502 3.1 19.6 1.0
CE1 C:HIS442 3.3 19.0 1.0
CG C:HIS442 3.4 17.4 1.0
HE1 C:HIS442 3.5 22.8 1.0
H52 C:HCA502 3.5 23.9 1.0
CX C:ICS503 3.6 11.8 1.0
CB C:HIS442 3.7 16.8 1.0
H22 C:HCA502 4.0 22.9 1.0
O C:HOH682 4.1 20.1 1.0
C2 C:HCA502 4.1 19.1 1.0
O1 C:HCA502 4.2 24.0 1.0
O6 C:HCA502 4.2 18.0 1.0
C4 C:HCA502 4.2 18.7 1.0
HA C:HIS442 4.3 20.5 1.0
C5 C:HCA502 4.4 19.9 1.0
HB2 C:HIS442 4.4 20.2 1.0
NE2 C:HIS442 4.5 17.9 1.0
H41 C:HCA502 4.5 22.5 1.0
HG22 C:ILE355 4.5 21.6 1.0
CD2 C:HIS442 4.5 16.1 1.0
CA C:HIS442 4.6 17.1 1.0
C1 C:HCA502 4.6 23.2 1.0
S2B C:ICS503 4.8 16.2 0.9
S5A C:ICS503 4.8 16.5 0.9
H51 C:HCA502 4.8 23.9 1.0
HA3 C:GLY356 4.9 20.3 1.0
S3A C:ICS503 4.9 16.6 1.0
FE2 C:ICS503 5.0 16.9 1.0

Reference:

S.M.Keable, J.Vertemara, O.A.Zadvornyy, B.J.Eilers, K.Danyal, A.J.Rasmussen, L.De Gioia, G.Zampella, L.C.Seefeldt, J.W.Peters. Structural Characterization of the Nitrogenase Molybdenum-Iron Protein with the Substrate Acetylene Trapped Near the Active Site. J. Inorg. Biochem. V. 180 129 2017.
ISSN: ISSN 1873-3344
PubMed: 29275221
DOI: 10.1016/J.JINORGBIO.2017.12.008
Page generated: Tue Dec 15 05:20:13 2020

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