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Zinc in PDB 1rfu: Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp

Enzymatic activity of Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp

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

Protein crystallography data

The structure of Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp, PDB code: 1rfu 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 43
Cell size a, b, c (Å), α, β, γ (°) 109.088, 109.088, 284.272, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp (pdb code 1rfu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp, PDB code: 1rfu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1rfu

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Zinc binding site 1 out of 8 in the Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp


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 and Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:48.9
occ:1.00
 O1P A:PLP401 2.5 43.4 1.0
O1B A:ADP402 2.6 31.4 1.0
O3P A:PLP401 3.3 44.0 1.0
P A:PLP401 3.3 44.7 1.0
PB A:ADP402 3.4 33.5 1.0
OH A:TYR127 3.5 37.1 1.0
O3B A:ADP402 3.5 30.8 1.0
CG2 A:VAL115 3.7 28.1 1.0
OE2 A:GLU153 3.9 41.2 1.0
O2B A:ADP402 4.1 31.2 1.0
OD1 A:ASP113 4.1 34.5 1.0
O4P A:PLP401 4.2 35.5 1.0
C5A A:PLP401 4.3 27.4 1.0
OE1 A:GLU153 4.3 43.0 1.0
CA A:GLY234 4.4 31.8 1.0
CG1 A:VAL115 4.4 27.0 1.0
OD2 A:ASP113 4.4 32.6 1.0
CB A:VAL115 4.5 26.0 1.0
CD A:GLU153 4.5 42.8 1.0
CA A:VAL115 4.6 27.1 1.0
CG A:ASP113 4.7 32.5 1.0
O2P A:PLP401 4.7 45.0 1.0
CZ A:TYR127 4.8 37.2 1.0
O3A A:ADP402 4.8 29.1 1.0
OD1 A:ASN150 4.9 42.2 1.0
OD2 A:ASP235 5.0 32.8 1.0

Zinc binding site 2 out of 8 in 1rfu

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Zinc binding site 2 out of 8 in the Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp


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 and Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1403

b:54.1
occ:1.00
 O1P B:PLP1401 2.4 37.7 1.0
O1B B:ADP1402 2.4 32.3 1.0
CG2 B:VAL115 3.3 24.4 1.0
P B:PLP1401 3.5 40.0 1.0
O3P B:PLP1401 3.7 37.2 1.0
OD1 B:ASP113 3.7 33.8 1.0
OH B:TYR127 3.8 35.2 1.0
PB B:ADP1402 3.9 32.5 1.0
OE2 B:GLU153 4.0 39.0 1.0
OD2 B:ASP113 4.1 32.0 1.0
CB B:VAL115 4.2 23.3 1.0
CG1 B:VAL115 4.2 23.6 1.0
CG B:ASP113 4.2 31.3 1.0
OE1 B:GLU153 4.4 40.1 1.0
CA B:GLY234 4.4 27.9 1.0
CA B:VAL115 4.4 25.2 1.0
C5A B:PLP1401 4.4 28.0 1.0
O4P B:PLP1401 4.4 32.9 1.0
O3B B:ADP1402 4.5 32.6 1.0
CD B:GLU153 4.6 38.0 1.0
O2B B:ADP1402 4.6 30.0 1.0
O2P B:PLP1401 4.8 39.9 1.0
O3A B:ADP1402 4.8 28.1 1.0
OD1 B:ASP235 4.8 30.8 1.0
OD2 B:ASP235 4.9 28.1 1.0
N B:ASP235 4.9 28.7 1.0
C B:GLY234 4.9 29.2 1.0

Zinc binding site 3 out of 8 in 1rfu

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Zinc binding site 3 out of 8 in the Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2403

b:49.7
occ:1.00
 O1B C:ADP2402 2.0 33.0 1.0
O1P C:PLP2401 2.3 54.4 1.0
P C:PLP2401 3.4 55.1 1.0
PB C:ADP2402 3.4 35.7 1.0
O3P C:PLP2401 3.5 53.6 1.0
CG2 C:VAL115 3.7 31.6 1.0
OD1 C:ASP113 3.7 36.3 1.0
O3B C:ADP2402 4.0 36.0 1.0
CA C:GLY234 4.0 30.2 1.0
OD2 C:ASP113 4.0 38.5 1.0
OH C:TYR127 4.0 25.6 1.0
CG C:ASP113 4.2 37.0 1.0
OE2 C:GLU153 4.3 45.7 1.0
O2B C:ADP2402 4.3 33.5 1.0
O3A C:ADP2402 4.4 35.5 1.0
O4P C:PLP2401 4.4 51.7 1.0
OE1 C:GLU153 4.5 45.2 1.0
C5A C:PLP2401 4.5 49.3 1.0
O2P C:PLP2401 4.5 55.2 1.0
C C:GLY234 4.5 31.4 1.0
CB C:VAL115 4.6 31.5 1.0
N C:ASP235 4.6 30.7 1.0
CG1 C:VAL115 4.7 31.8 1.0
CA C:VAL115 4.8 32.9 1.0
N C:GLY234 4.8 29.1 1.0
CD C:GLU153 4.8 44.2 1.0
OD2 C:ASP235 4.8 29.8 1.0
OD1 C:ASP235 5.0 29.8 1.0

Zinc binding site 4 out of 8 in 1rfu

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Zinc binding site 4 out of 8 in the Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn3403

b:45.2
occ:1.00
 O1B D:ADP3402 2.2 49.7 1.0
O1P D:PLP3401 2.5 54.8 1.0
P D:PLP3401 3.5 56.5 1.0
CG2 D:VAL115 3.5 41.0 1.0
OD1 D:ASP113 3.5 42.5 1.0
O3P D:PLP3401 3.6 54.6 1.0
PB D:ADP3402 3.7 51.0 1.0
OD2 D:ASP113 3.8 40.6 1.0
CG D:ASP113 4.0 41.5 1.0
CA D:GLY234 4.0 28.9 1.0
OH D:TYR127 4.2 47.4 1.0
OE2 D:GLU153 4.3 50.5 1.0
O3B D:ADP3402 4.3 50.8 1.0
OE1 D:GLU153 4.3 51.1 1.0
O2B D:ADP3402 4.4 50.5 1.0
CB D:VAL115 4.5 39.1 1.0
C D:GLY234 4.6 30.0 1.0
O3A D:ADP3402 4.6 47.1 1.0
O4P D:PLP3401 4.6 51.9 1.0
CA D:VAL115 4.6 39.8 1.0
N D:ASP235 4.6 30.9 1.0
CG1 D:VAL115 4.6 38.3 1.0
C5A D:PLP3401 4.7 47.4 1.0
O2P D:PLP3401 4.7 55.6 1.0
CD D:GLU153 4.7 50.5 1.0
OD2 D:ASP235 4.8 31.1 1.0
N D:GLY234 4.9 28.2 1.0
OD1 D:ASP235 4.9 29.6 1.0

Zinc binding site 5 out of 8 in 1rfu

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Zinc binding site 5 out of 8 in the Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn4403

b:59.9
occ:1.00
 O1P E:PLP4401 2.2 26.4 1.0
O1B E:ADP4402 2.3 28.4 1.0
CG2 E:VAL115 3.3 13.8 1.0
P E:PLP4401 3.4 25.5 1.0
OD1 E:ASP113 3.5 25.7 1.0
O3P E:PLP4401 3.6 21.0 1.0
PB E:ADP4402 3.7 32.9 1.0
OD2 E:ASP113 3.8 25.3 1.0
OH E:TYR127 4.0 32.9 1.0
CG E:ASP113 4.1 25.9 1.0
CA E:GLY234 4.1 27.1 1.0
OE2 E:GLU153 4.3 43.3 1.0
CB E:VAL115 4.3 17.1 1.0
CG1 E:VAL115 4.3 16.7 1.0
O4P E:PLP4401 4.4 18.0 1.0
O3B E:ADP4402 4.4 31.7 1.0
C5A E:PLP4401 4.4 13.4 1.0
O2B E:ADP4402 4.5 29.8 1.0
OE1 E:GLU153 4.6 41.3 1.0
CA E:VAL115 4.6 20.2 1.0
O2P E:PLP4401 4.6 25.6 1.0
C E:GLY234 4.6 27.0 1.0
N E:ASP235 4.7 26.5 1.0
O3A E:ADP4402 4.7 30.6 1.0
OD2 E:ASP235 4.7 24.6 1.0
CD E:GLU153 4.8 41.1 1.0
N E:GLY234 4.9 26.2 1.0

Zinc binding site 6 out of 8 in 1rfu

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Zinc binding site 6 out of 8 in the Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn5403

b:52.5
occ:1.00
 O1B F:ADP5402 2.3 33.0 1.0
O1P F:PLP5401 2.4 31.5 1.0
O3P F:PLP5401 3.2 25.4 1.0
OD1 F:ASP113 3.2 31.4 1.0
P F:PLP5401 3.3 28.9 1.0
CG2 F:VAL115 3.5 22.5 1.0
PB F:ADP5402 3.7 37.1 1.0
CA F:GLY234 3.7 28.2 1.0
OD2 F:ASP113 3.8 29.9 1.0
CG F:ASP113 3.9 30.3 1.0
N F:ASP235 4.2 27.2 1.0
C F:GLY234 4.2 27.8 1.0
O3B F:ADP5402 4.2 35.3 1.0
OD2 F:ASP235 4.3 19.6 1.0
O4P F:PLP5401 4.4 23.9 1.0
OH F:TYR127 4.4 17.1 1.0
C5A F:PLP5401 4.4 19.4 1.0
O2P F:PLP5401 4.5 29.4 1.0
N F:GLY234 4.5 27.5 1.0
CB F:VAL115 4.5 22.3 1.0
O3A F:ADP5402 4.6 33.4 1.0
CG F:ASP235 4.6 22.3 1.0
OD1 F:ASP235 4.6 25.0 1.0
CG1 F:VAL115 4.7 22.4 1.0
O2B F:ADP5402 4.7 34.7 1.0
OE2 F:GLU153 4.7 33.0 1.0
CA F:VAL115 4.9 24.9 1.0
OE1 F:GLU153 4.9 33.2 1.0

Zinc binding site 7 out of 8 in 1rfu

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Zinc binding site 7 out of 8 in the Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn6403

b:85.7
occ:1.00
 O1B G:ADP6402 1.9 33.5 1.0
O1P G:PLP6401 2.2 40.7 1.0
P G:PLP6401 3.1 41.8 1.0
O3P G:PLP6401 3.2 39.2 1.0
PB G:ADP6402 3.4 36.6 1.0
OD1 G:ASP113 3.6 23.9 1.0
CG2 G:VAL115 3.7 26.4 1.0
CA G:GLY234 3.7 31.9 1.0
O3B G:ADP6402 3.9 35.7 1.0
OD2 G:ASP113 4.0 23.0 1.0
OH G:TYR127 4.1 33.9 1.0
CG G:ASP113 4.2 24.7 1.0
O2B G:ADP6402 4.2 34.3 1.0
O4P G:PLP6401 4.3 37.7 1.0
C G:GLY234 4.3 31.3 1.0
O3A G:ADP6402 4.3 36.3 1.0
O2P G:PLP6401 4.3 42.3 1.0
N G:ASP235 4.4 30.1 1.0
C5A G:PLP6401 4.5 34.3 1.0
N G:GLY234 4.5 32.6 1.0
OE2 G:GLU153 4.6 47.9 1.0
OD2 G:ASP235 4.7 28.7 1.0
OE1 G:GLU153 4.7 46.8 1.0
CB G:VAL115 4.7 28.2 1.0
CG1 G:VAL115 4.8 27.4 1.0
OD1 G:ASP235 4.9 29.0 1.0
CG G:ASP235 4.9 27.3 1.0
CA G:VAL115 5.0 30.4 1.0

Zinc binding site 8 out of 8 in 1rfu

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Zinc binding site 8 out of 8 in the Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Pyridoxal Kinase Complexed with Adp and Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn7403

b:59.1
occ:1.00
 O1B H:ADP7402 2.1 51.7 1.0
O1P H:PLP7401 2.6 33.7 1.0
CG2 H:VAL115 3.4 40.0 1.0
OD1 H:ASP113 3.5 44.4 1.0
P H:PLP7401 3.6 32.9 1.0
PB H:ADP7402 3.6 53.3 1.0
O3P H:PLP7401 3.6 31.1 1.0
OD2 H:ASP113 3.7 44.2 1.0
CG H:ASP113 4.0 43.9 1.0
CA H:GLY234 4.0 39.4 1.0
O3B H:ADP7402 4.3 53.3 1.0
OH H:TYR127 4.3 32.0 1.0
OE2 H:GLU153 4.4 37.2 1.0
CB H:VAL115 4.4 40.4 1.0
C H:GLY234 4.4 39.8 1.0
O2B H:ADP7402 4.5 53.5 1.0
O3A H:ADP7402 4.5 52.2 1.0
N H:ASP235 4.5 40.2 1.0
OE1 H:GLU153 4.5 35.9 1.0
CG1 H:VAL115 4.6 40.1 1.0
O4P H:PLP7401 4.6 30.2 1.0
OD2 H:ASP235 4.6 38.0 1.0
CA H:VAL115 4.6 40.9 1.0
C5A H:PLP7401 4.7 27.9 1.0
O2P H:PLP7401 4.8 32.0 1.0
N H:GLY234 4.8 39.1 1.0
CD H:GLU153 4.9 36.6 1.0
OD1 H:ASP235 4.9 38.5 1.0
CG H:ASP235 4.9 38.2 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 Oct 16 18:33:52 2024

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