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Magnesium in PDB 3vkb: Crystal Structure of MOEO5 Soaked with Fspp Overnight

Protein crystallography data

The structure of Crystal Structure of MOEO5 Soaked with Fspp Overnight, PDB code: 3vkb was solved by F.Ren, T.-P.Ko, C.-H.Huang, R.-T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.677, 58.564, 58.899, 97.67, 112.24, 108.56
R / Rfree (%) 16.1 / 19.2

Other elements in 3vkb:

The structure of Crystal Structure of MOEO5 Soaked with Fspp Overnight also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of MOEO5 Soaked with Fspp Overnight (pdb code 3vkb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of MOEO5 Soaked with Fspp Overnight, PDB code: 3vkb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3vkb

Go back to Magnesium Binding Sites List in 3vkb
Magnesium binding site 1 out of 3 in the Crystal Structure of MOEO5 Soaked with Fspp Overnight


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of MOEO5 Soaked with Fspp Overnight within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:26.1
occ:1.00
O B:LEU137 2.6 15.1 1.0
O A:LEU137 2.7 14.8 1.0
O A:ALA138 2.7 15.5 1.0
O A:PHE140 2.8 20.8 1.0
O B:ALA138 2.8 17.3 1.0
O B:PHE140 2.8 20.8 1.0
C A:ALA138 3.3 15.6 1.0
C B:ALA138 3.3 16.0 1.0
CA A:ALA138 3.6 13.0 1.0
CA B:ALA138 3.6 14.9 1.0
C B:LEU137 3.7 14.4 1.0
C A:LEU137 3.8 14.1 1.0
C A:PHE140 3.8 20.6 1.0
C B:PHE140 3.8 22.2 1.0
N A:PHE140 3.9 19.5 1.0
N B:PHE140 3.9 17.3 1.0
O B:HOH428 4.2 34.1 1.0
N A:ALA138 4.2 12.7 1.0
N B:ALA138 4.2 12.9 1.0
CA A:PHE140 4.2 19.0 1.0
CB B:PHE140 4.2 18.3 1.0
CA B:PHE140 4.2 17.9 1.0
O B:HOH374 4.3 32.6 1.0
CB A:PHE140 4.3 18.6 1.0
CD2 B:PHE140 4.3 22.5 1.0
N A:ALA139 4.3 16.4 1.0
N B:ALA139 4.3 15.8 1.0
CD2 A:PHE140 4.3 17.6 1.0
C A:ALA139 4.5 18.7 1.0
C B:ALA139 4.5 19.1 1.0
CG B:PHE140 4.8 20.6 1.0
CA A:ALA139 4.8 17.9 1.0
CG A:PHE140 4.8 17.3 1.0
CA B:ALA139 4.9 16.6 1.0
CB A:ALA138 4.9 15.8 1.0
CB B:ALA138 5.0 15.7 1.0
N A:PRO141 5.0 21.8 1.0

Magnesium binding site 2 out of 3 in 3vkb

Go back to Magnesium Binding Sites List in 3vkb
Magnesium binding site 2 out of 3 in the Crystal Structure of MOEO5 Soaked with Fspp Overnight


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of MOEO5 Soaked with Fspp Overnight within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:30.5
occ:1.00
O4 A:POP800 2.0 39.0 1.0
O A:HOH495 2.1 25.7 1.0
O1 A:POP800 2.1 35.2 1.0
OD2 A:ASP41 2.1 17.3 1.0
OG A:SER69 2.2 19.1 1.0
OD1 A:ASP71 2.3 25.9 1.0
CG A:ASP41 3.1 14.3 1.0
CG A:ASP71 3.2 26.1 1.0
P2 A:POP800 3.3 44.1 1.0
P1 A:POP800 3.3 40.8 1.0
CB A:SER69 3.4 13.8 1.0
OD2 A:ASP71 3.5 28.7 1.0
OD1 A:ASP41 3.5 14.0 1.0
O A:POP800 3.7 41.8 1.0
CA A:SER69 3.9 12.6 1.0
O2 A:POP800 3.9 41.8 1.0
N A:THR70 4.0 15.0 1.0
O5 A:POP800 4.2 44.2 1.0
N A:ASP71 4.2 18.1 1.0
O6 A:POP800 4.4 43.0 1.0
C A:SER69 4.4 12.7 1.0
O A:ASP71 4.4 17.4 1.0
CB A:ASP41 4.4 12.6 1.0
O A:HOH404 4.5 32.2 1.0
O3 A:POP800 4.5 38.3 1.0
CB A:ASP71 4.5 22.1 1.0
CE A:LYS44 4.8 27.7 1.0
O A:HOH494 4.8 31.0 1.0
CA A:ASP71 4.9 19.3 1.0
O A:HOH295 5.0 38.9 1.0

Magnesium binding site 3 out of 3 in 3vkb

Go back to Magnesium Binding Sites List in 3vkb
Magnesium binding site 3 out of 3 in the Crystal Structure of MOEO5 Soaked with Fspp Overnight


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of MOEO5 Soaked with Fspp Overnight within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:20.8
occ:1.00
O1 B:POP800 1.9 31.3 1.0
O4 B:POP800 2.1 34.7 1.0
O B:HOH335 2.1 22.2 1.0
OD1 B:ASP71 2.1 20.5 1.0
OD2 B:ASP41 2.2 16.3 1.0
OG B:SER69 2.2 16.3 1.0
CG B:ASP41 3.1 12.8 1.0
CG B:ASP71 3.2 21.9 1.0
P1 B:POP800 3.2 36.5 1.0
CB B:SER69 3.4 15.4 1.0
OD1 B:ASP41 3.4 11.9 1.0
P2 B:POP800 3.4 39.5 1.0
OD2 B:ASP71 3.5 23.9 1.0
O B:POP800 3.7 37.3 1.0
O2 B:POP800 3.9 39.4 1.0
CA B:SER69 3.9 12.2 1.0
N B:THR70 3.9 14.0 1.0
N B:ASP71 4.1 17.7 1.0
O B:ASP71 4.3 16.4 1.0
C B:SER69 4.3 13.0 1.0
O3 B:POP800 4.4 33.1 1.0
O6 B:POP800 4.4 39.5 1.0
O5 B:POP800 4.5 38.9 1.0
CB B:ASP71 4.5 18.4 1.0
CB B:ASP41 4.5 13.1 1.0
NH2 B:ARG165 4.5 36.1 1.0
O B:HOH408 4.8 26.6 1.0
CA B:ASP71 4.8 17.1 1.0
CA B:THR70 5.0 14.0 1.0
CE B:LYS44 5.0 27.9 1.0
C B:ASP71 5.0 17.2 1.0

Reference:

F.Ren, T.-P.Ko, X.Feng, C.-H.Huang, H.-C.Chan, Y.Hu, K.Wang, Y.Ma, P.-H.Liang, A.H.-J.Wang, E.Oldfield, R.-T.Guo. Insights Into the Mechanism of the Antibiotic-Synthesizing Enzyme MOEO5 From Crystal Structures of Different Complexes Angew.Chem.Int.Ed.Engl. V. 51 4157 2012.
ISSN: ISSN 1433-7851
PubMed: 22431288
DOI: 10.1002/ANIE.201108002
Page generated: Mon Dec 14 08:59:16 2020

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