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Zinc in PDB 1rfv: Crystal Structure of Pyridoxal Kinase Complexed with Adp

Enzymatic activity of Crystal Structure of Pyridoxal Kinase Complexed with Adp

All present enzymatic activity of Crystal Structure of Pyridoxal Kinase Complexed with Adp:
2.7.1.35;

Protein crystallography data

The structure of Crystal Structure of Pyridoxal Kinase Complexed with Adp, PDB code: 1rfv was solved by D.-C.Liang, T.Jiang, M.-H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.066, 93.942, 128.743, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Pyridoxal Kinase Complexed with Adp (pdb code 1rfv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Pyridoxal Kinase Complexed with Adp, PDB code: 1rfv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1rfv

Go back to Zinc Binding Sites List in 1rfv
Zinc binding site 1 out of 2 in the Crystal Structure of Pyridoxal Kinase Complexed with Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Pyridoxal Kinase Complexed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:55.5
occ:1.00
O2B A:ADP401 2.0 54.0 1.0
PB A:ADP401 3.2 58.1 1.0
O A:HOH404 3.3 40.2 1.0
O3B A:ADP401 3.5 51.2 1.0
OE1 A:GLN119 3.5 65.5 1.0
O3A A:ADP401 3.6 52.7 1.0
OD1 A:ASP113 3.7 29.5 1.0
OD2 A:ASP113 3.7 30.1 1.0
OE2 A:GLU153 4.0 38.5 1.0
CG2 A:VAL115 4.1 28.6 1.0
CD A:GLN119 4.2 63.4 1.0
CG A:ASP113 4.2 28.2 1.0
NE2 A:GLN119 4.2 65.3 1.0
OE1 A:GLU153 4.2 37.9 1.0
ND2 A:ASN150 4.5 32.6 1.0
O1B A:ADP401 4.5 54.2 1.0
CD A:GLU153 4.6 37.5 1.0
CA A:GLY234 4.7 15.8 1.0
CG1 A:VAL115 4.9 26.1 1.0
PA A:ADP401 4.9 55.2 1.0
CB A:VAL115 4.9 30.0 1.0

Zinc binding site 2 out of 2 in 1rfv

Go back to Zinc Binding Sites List in 1rfv
Zinc binding site 2 out of 2 in the Crystal Structure of Pyridoxal Kinase Complexed with Adp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Pyridoxal Kinase Complexed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1402

b:40.8
occ:1.00
O2B B:ADP1401 2.0 42.7 1.0
O B:HOH1403 3.2 8.9 1.0
PB B:ADP1401 3.5 44.4 1.0
OD2 B:ASP113 3.7 22.8 1.0
OD1 B:ASP113 3.8 25.2 1.0
O3A B:ADP1401 3.9 41.8 1.0
O3B B:ADP1401 4.0 42.8 1.0
OE2 B:GLU153 4.0 36.5 1.0
O B:HOH1459 4.1 48.2 1.0
CG B:ASP113 4.2 22.9 1.0
OE1 B:GLU153 4.2 36.7 1.0
CG2 B:VAL115 4.3 22.4 1.0
ND2 B:ASN150 4.4 27.7 1.0
O B:HOH1421 4.5 35.9 1.0
CD B:GLU153 4.6 35.5 1.0
O1B B:ADP1401 4.6 47.1 1.0
CA B:GLY234 4.7 12.7 1.0
O B:HOH1442 4.8 35.2 1.0
CG1 B:VAL115 4.8 23.2 1.0
CB B:VAL115 5.0 25.3 1.0

Reference:

M.-H.Li, F.Kwok, W.-R.Chang, S.-Q.Liu, S.C.L.Lo, J.-P.Zhang, T.Jiang, D.-C.Liang. Conformational Changes in the Reaction of Pyridoxal Kinase J.Biol.Chem. V. 279 17459 2004.
ISSN: ISSN 0021-9258
PubMed: 14722069
DOI: 10.1074/JBC.M312380200
Page generated: Wed Dec 16 03:02:54 2020

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