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Nickel in PDB 1vkl: Rabbit Muscle Phosphoglucomutase

Enzymatic activity of Rabbit Muscle Phosphoglucomutase

All present enzymatic activity of Rabbit Muscle Phosphoglucomutase:
5.4.2.2;

Protein crystallography data

The structure of Rabbit Muscle Phosphoglucomutase, PDB code: 1vkl was solved by W.J.Ray Junior, S.Baranidharan, Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 174.420, 174.420, 101.120, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21

Nickel Binding Sites:

The binding sites of Nickel atom in the Rabbit Muscle Phosphoglucomutase (pdb code 1vkl). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Rabbit Muscle Phosphoglucomutase, PDB code: 1vkl:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1vkl

Go back to Nickel Binding Sites List in 1vkl
Nickel binding site 1 out of 2 in the Rabbit Muscle Phosphoglucomutase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Rabbit Muscle Phosphoglucomutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni562

b:42.4
occ:1.00
OD1 A:ASP287 2.0 27.5 1.0
OD2 A:ASP289 2.1 25.2 1.0
O2P A:SEP116 2.1 39.6 1.0
OD1 A:ASP291 2.2 34.0 1.0
OG A:SEP116 2.9 39.4 1.0
P A:SEP116 3.1 39.3 1.0
CG A:ASP287 3.1 28.8 1.0
CG A:ASP289 3.2 25.4 1.0
CB A:SEP116 3.3 32.2 1.0
CG A:ASP291 3.4 30.9 1.0
OD2 A:ASP287 3.6 32.9 1.0
OD1 A:ASP289 3.7 27.1 1.0
O3P A:SEP116 4.0 37.9 1.0
CA A:SEP116 4.1 27.0 1.0
O1P A:SEP116 4.1 38.8 1.0
N A:ASP291 4.2 22.9 1.0
CB A:ASP291 4.3 25.7 1.0
CB A:ASP287 4.3 23.3 1.0
OD2 A:ASP291 4.3 34.8 1.0
NE A:ARG292 4.4 19.1 1.0
N A:ASP289 4.4 19.1 1.0
CB A:ASP289 4.5 21.9 1.0
CA A:ASP291 4.6 22.7 1.0
N A:ARG292 4.7 18.7 1.0
CG A:ARG292 4.7 18.9 1.0
C A:SEP116 4.8 27.4 1.0
NZ A:LYS388 4.8 36.6 1.0
CA A:ASP289 4.8 19.2 1.0
C A:ASP291 4.8 21.1 1.0
N A:HIS117 4.9 28.9 1.0
CB A:ARG292 4.9 18.6 1.0
N A:GLY290 4.9 17.0 1.0
C A:ASP289 5.0 17.1 1.0
CD A:ARG292 5.0 18.5 1.0

Nickel binding site 2 out of 2 in 1vkl

Go back to Nickel Binding Sites List in 1vkl
Nickel binding site 2 out of 2 in the Rabbit Muscle Phosphoglucomutase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Rabbit Muscle Phosphoglucomutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni562

b:32.0
occ:1.00
O B:HOH706 2.0 30.2 1.0
OD2 B:ASP287 2.0 20.2 1.0
OD2 B:ASP289 2.1 21.4 1.0
OD2 B:ASP291 2.1 19.6 1.0
O2P B:SEP116 2.1 34.0 1.0
CB B:SEP116 2.9 26.8 1.0
CG B:ASP289 3.1 19.3 1.0
CG B:ASP291 3.1 17.1 1.0
CG B:ASP287 3.1 22.0 1.0
P B:SEP116 3.4 38.2 1.0
OD1 B:ASP289 3.5 17.3 1.0
OD1 B:ASP291 3.6 17.8 1.0
OD1 B:ASP287 3.7 25.5 1.0
OG B:SEP116 3.7 35.5 1.0
CA B:SEP116 3.9 22.2 1.0
O1P B:SEP116 4.1 35.2 1.0
N B:ASP291 4.2 15.5 1.0
CB B:ASP291 4.3 12.8 1.0
NE B:ARG292 4.4 14.6 1.0
CB B:ASP287 4.4 17.9 1.0
CB B:ASP289 4.4 16.3 1.0
O3P B:SEP116 4.5 38.2 1.0
N B:ASP289 4.5 14.3 1.0
N B:ARG292 4.6 10.5 1.0
CG B:ARG292 4.6 10.2 1.0
C B:SEP116 4.6 20.2 1.0
CA B:ASP291 4.7 13.3 1.0
CA B:ASP289 4.8 15.8 1.0
N B:HIS117 4.8 21.7 1.0
C B:ASP291 4.9 11.7 1.0
N B:GLY290 4.9 14.3 1.0
C B:ASP289 4.9 15.6 1.0
CB B:ARG292 4.9 9.9 1.0
CD B:ARG292 4.9 11.1 1.0

Reference:

W.J.Ray Jr., C.B.Post, Y.Liu, G.I.Rhyu. Structural Changes at the Metal Ion Binding Site During the Phosphoglucomutase Reaction. Biochemistry V. 32 48 1993.
ISSN: ISSN 0006-2960
PubMed: 8418859
DOI: 10.1021/BI00052A008
Page generated: Fri Sep 25 08:03:05 2020
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