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Magnesium in PDB 5h5x: Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor

Protein crystallography data

The structure of Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor, PDB code: 5h5x was solved by X.-D.Kong, J.-H.Xu, J.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.50 / 2.30
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 187.787, 187.787, 80.858, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor (pdb code 5h5x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor, PDB code: 5h5x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5h5x

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Magnesium binding site 1 out of 6 in the Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor


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 Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:38.4
occ:1.00
 OXT C:VAL263 2.0 31.5 1.0
O A:HOH415 2.0 28.5 1.0
O C:HOH442 2.1 32.1 1.0
O A:HOH476 2.3 29.0 1.0
O A:HOH423 2.4 25.8 1.0
O A:VAL263 2.5 30.6 1.0
C C:VAL263 2.8 33.6 1.0
O C:VAL263 2.9 29.1 1.0
C A:VAL263 3.4 31.5 1.0
OXT A:VAL263 3.6 25.8 1.0
O C:HOH438 3.8 30.8 1.0
CA C:VAL263 4.2 34.7 1.0
O C:TYR260 4.3 30.7 1.0
O A:TYR260 4.5 29.4 1.0
O C:HOH446 4.5 31.2 1.0
N C:VAL263 4.5 27.4 1.0
CG2 C:VAL263 4.6 29.1 1.0
O A:THR261 4.8 34.1 1.0
CA A:VAL263 4.8 31.9 1.0
CB C:VAL263 4.8 31.9 1.0
O A:HOH409 4.8 33.0 1.0
CG2 A:VAL263 4.9 27.9 1.0
O C:THR261 5.0 35.5 1.0

Magnesium binding site 2 out of 6 in 5h5x

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Magnesium binding site 2 out of 6 in the Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor


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 Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:36.4
occ:1.00
 O B:HOH413 1.9 25.4 1.0
O B:HOH409 1.9 30.9 1.0
O D:VAL263 2.0 25.5 1.0
O B:HOH423 2.2 26.7 1.0
O B:HOH475 2.2 28.3 1.0
O B:VAL263 2.3 25.3 1.0
C D:VAL263 2.9 30.8 1.0
OXT D:VAL263 3.2 28.2 1.0
C B:VAL263 3.3 29.0 1.0
OXT B:VAL263 3.5 26.0 1.0
O B:HOH417 3.9 29.9 1.0
O B:TYR260 4.2 30.8 1.0
CA D:VAL263 4.3 29.3 1.0
O D:TYR260 4.5 22.5 1.0
O B:HOH450 4.5 33.1 1.0
CA B:VAL263 4.6 25.5 1.0
O B:HOH428 4.6 29.7 1.0
N D:VAL263 4.6 28.1 1.0
CG2 D:VAL263 4.8 25.7 1.0
CG1 B:VAL162 4.8 21.3 1.0
N B:VAL263 4.9 28.4 1.0
CG2 B:VAL263 4.9 23.1 1.0
O D:THR261 4.9 34.2 1.0
CA B:THR261 4.9 26.9 1.0

Magnesium binding site 3 out of 6 in 5h5x

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Magnesium binding site 3 out of 6 in the Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor


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 Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:30.7
occ:1.00
 O G:HOH433 1.9 27.3 1.0
OXT G:VAL263 2.0 29.3 1.0
O G:HOH460 2.1 37.0 1.0
O G:HOH432 2.2 26.3 1.0
O G:HOH424 2.2 33.4 1.0
O E:VAL263 2.3 27.4 1.0
C G:VAL263 3.0 30.5 1.0
C E:VAL263 3.2 29.6 1.0
O G:VAL263 3.3 30.8 1.0
OXT E:VAL263 3.4 26.3 1.0
O G:HOH404 3.9 27.2 1.0
O G:TYR260 4.3 27.6 1.0
O E:HOH452 4.4 29.8 1.0
CA G:VAL263 4.4 30.8 1.0
O E:TYR260 4.4 31.8 1.0
O G:THR261 4.6 32.2 1.0
CA E:VAL263 4.6 25.4 1.0
N G:VAL263 4.6 28.3 1.0
CG1 G:VAL162 4.6 27.9 1.0
CA G:THR261 4.6 28.8 1.0
O G:HOH421 4.7 25.9 1.0
CG1 E:VAL162 4.7 32.6 1.0
C G:THR261 4.8 30.9 1.0
N E:VAL263 4.8 30.1 1.0
O E:THR261 4.9 29.3 1.0
CA E:THR261 4.9 28.8 1.0

Magnesium binding site 4 out of 6 in 5h5x

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Magnesium binding site 4 out of 6 in the Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:28.5
occ:1.00
 O H:HOH426 2.0 29.1 1.0
O H:VAL263 2.1 29.5 1.0
O H:HOH421 2.1 24.4 1.0
O F:HOH418 2.2 27.7 1.0
O F:VAL263 2.2 29.9 1.0
O H:HOH451 2.5 36.8 1.0
C H:VAL263 3.1 29.8 1.0
C F:VAL263 3.3 27.7 1.0
OXT H:VAL263 3.5 30.2 1.0
OXT F:VAL263 3.6 26.4 1.0
O H:THR261 4.3 26.0 1.0
O H:HOH415 4.3 25.1 1.0
CA H:VAL263 4.4 26.6 1.0
O F:THR261 4.5 29.5 1.0
O H:TYR260 4.5 29.8 1.0
O F:HOH433 4.6 24.2 1.0
N H:VAL263 4.6 25.3 1.0
CA F:VAL263 4.6 28.2 1.0
CG1 H:VAL162 4.6 30.4 1.0
O F:TYR260 4.6 23.1 1.0
C H:THR261 4.7 30.2 1.0
CG1 F:VAL162 4.7 27.1 1.0
CA H:THR261 4.7 25.3 1.0
N F:VAL263 4.8 26.8 1.0
C F:THR261 4.9 25.6 1.0
CA F:THR261 4.9 24.4 1.0

Magnesium binding site 5 out of 6 in 5h5x

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Magnesium binding site 5 out of 6 in the Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:37.0
occ:1.00
 O I:HOH414 2.2 26.2 1.0
O K:HOH404 2.2 28.3 1.0
OXT K:VAL263 2.3 32.0 1.0
O K:HOH456 2.5 30.6 1.0
O I:VAL263 2.6 33.4 1.0
C K:VAL263 3.0 36.9 1.0
O K:VAL263 3.0 33.4 1.0
OXT I:VAL263 3.3 23.7 1.0
C I:VAL263 3.3 33.0 1.0
O K:HOH449 3.6 31.7 1.0
O K:HOH455 4.2 31.2 1.0
O K:TYR260 4.3 29.3 1.0
O I:HOH415 4.4 30.4 1.0
CA K:VAL263 4.4 33.2 1.0
O I:TYR260 4.5 33.2 1.0
CG2 I:VAL263 4.6 28.8 1.0
CG2 K:VAL263 4.6 38.6 1.0
CA I:VAL263 4.7 30.9 1.0
N K:VAL263 4.8 29.6 1.0

Magnesium binding site 6 out of 6 in 5h5x

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Magnesium binding site 6 out of 6 in the Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg302

b:33.1
occ:1.00
 O J:HOH468 2.0 27.5 1.0
O J:HOH403 2.0 35.3 1.0
O J:HOH460 2.1 29.8 1.0
O J:VAL263 2.1 29.7 1.0
O J:HOH420 2.2 30.9 1.0
O L:VAL263 2.2 35.2 1.0
C L:VAL263 3.1 32.2 1.0
C J:VAL263 3.2 32.4 1.0
OXT L:VAL263 3.3 32.7 1.0
OXT J:VAL263 3.5 33.4 1.0
O L:HOH417 3.6 26.9 1.0
O J:HOH439 4.0 28.0 1.0
O J:TYR260 4.2 30.1 1.0
O J:HOH443 4.4 28.4 1.0
CA J:VAL263 4.4 30.1 1.0
CA L:VAL263 4.5 29.7 1.0
O L:TYR260 4.6 34.7 1.0
CG2 J:VAL263 4.6 25.0 1.0
N J:VAL263 4.7 27.6 1.0
O L:HOH421 4.8 33.0 1.0
N L:VAL263 4.9 34.5 1.0
O L:THR261 4.9 30.4 1.0
CG2 L:VAL263 4.9 29.2 1.0
O J:THR261 4.9 32.2 1.0

Reference:

M.Li, X.-D.Kong, J.Zhou, H.-L.Yu, Z.-J.Zhang, J.-H.Xu. Crystal Structure of Nadh Bound Carbonyl Reductase From Streptomyces Coelicolor To Be Published.
Page generated: Sun Sep 29 15:41:44 2024

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