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Zinc in PDB 7v1q: Leifsonia Alcohol Dehydrogenases Lnadh

Protein crystallography data

The structure of Leifsonia Alcohol Dehydrogenases Lnadh, PDB code: 7v1q was solved by Y.Song, X.Qu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.56 / 1.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.671, 238.522, 68.921, 90, 113.35, 90
R / Rfree (%) 16.4 / 19.5

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Leifsonia Alcohol Dehydrogenases Lnadh (pdb code 7v1q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Leifsonia Alcohol Dehydrogenases Lnadh, PDB code: 7v1q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in 7v1q

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Zinc binding site 1 out of 13 in the Leifsonia Alcohol Dehydrogenases Lnadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Leifsonia Alcohol Dehydrogenases Lnadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:12.4
occ:1.00
 O A:HOH436 2.0 16.6 1.0
O E:GLN251 2.1 6.5 0.5
O A:GLN251 2.1 6.1 0.5
O A:HOH430 2.1 10.3 1.0
O A:HOH487 2.1 12.6 1.0
O E:HOH427 2.2 10.2 1.0
C E:GLN251 3.0 10.7 0.5
C A:GLN251 3.0 10.9 0.5
C A:GLN251 3.1 10.9 0.5
C E:GLN251 3.1 10.2 0.5
O A:GLN251 3.4 5.6 0.5
O E:GLN251 3.4 6.1 0.5
O E:HOH516 4.3 20.9 1.0
O A:HOH493 4.4 18.5 1.0
CA E:GLN251 4.4 11.4 0.5
CA A:GLN251 4.4 11.4 0.5
CA E:GLN251 4.4 11.2 0.5
CA A:GLN251 4.4 11.5 0.5
O A:TYR248 4.5 9.1 1.0
O E:TYR248 4.5 7.6 1.0
CG1 A:VAL149 4.7 6.8 1.0
O A:THR249 4.7 10.7 1.0
O E:THR249 4.7 9.7 1.0
N A:GLN251 4.7 11.3 0.5
N E:GLN251 4.7 10.6 0.5
N A:GLN251 4.7 11.3 0.5
N E:GLN251 4.7 10.6 0.5
CG1 E:VAL149 4.7 7.3 1.0
CG E:GLN251 4.8 13.9 0.5
CA A:THR249 4.9 9.1 1.0
CG A:GLN251 4.9 13.8 0.5
CG E:GLN251 4.9 14.4 0.5
C A:THR249 4.9 9.5 1.0
CA E:THR249 4.9 8.1 1.0
C E:THR249 5.0 8.5 1.0
CG A:GLN251 5.0 15.1 0.5

Zinc binding site 2 out of 13 in 7v1q

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Zinc binding site 2 out of 13 in the Leifsonia Alcohol Dehydrogenases Lnadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Leifsonia Alcohol Dehydrogenases Lnadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:15.8
occ:1.00
 O A:HOH401 2.1 12.8 1.0
O A:HOH482 2.1 14.5 1.0
OE1 A:GLU43 2.1 11.0 1.0
O A:HOH440 2.2 12.5 1.0
CE1 G:HIS44 2.2 11.9 1.0
O G:HOH502 2.3 19.6 1.0
NE2 G:HIS44 2.9 13.1 1.0
CD A:GLU43 3.0 12.8 1.0
OE2 A:GLU43 3.2 17.0 1.0
ND1 G:HIS44 3.3 12.7 1.0
CD2 G:HIS44 4.2 11.4 1.0
O A:HOH491 4.2 26.4 1.0
O G:HOH511 4.2 22.9 1.0
OD1 G:ASN41 4.2 12.1 1.0
O A:HOH496 4.3 21.5 1.0
ND2 A:ASN41 4.3 9.2 1.0
CG G:HIS44 4.3 11.2 1.0
CG A:GLU43 4.4 12.0 1.0
N A:GLU42 4.4 10.6 1.0
N A:GLU43 4.5 10.6 1.0
CB A:GLU42 4.6 12.2 1.0
CB A:GLU43 4.8 11.0 1.0

Zinc binding site 3 out of 13 in 7v1q

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Zinc binding site 3 out of 13 in the Leifsonia Alcohol Dehydrogenases Lnadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Leifsonia Alcohol Dehydrogenases Lnadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:16.3
occ:1.00
 OE1 G:GLU43 2.1 13.0 1.0
NE2 A:HIS44 2.1 11.3 1.0
O G:HOH415 2.1 9.8 1.0
O G:HOH497 2.2 14.6 1.0
O G:HOH421 2.2 14.4 1.0
CE1 A:HIS44 2.9 11.3 1.0
CD G:GLU43 3.0 14.1 1.0
OE2 G:GLU43 3.2 17.4 1.0
CD2 A:HIS44 3.2 11.5 1.0
O G:HOH510 4.0 18.3 1.0
ND1 A:HIS44 4.1 11.9 1.0
CG A:HIS44 4.2 11.1 1.0
N G:GLU42 4.3 10.7 1.0
ND2 G:ASN41 4.3 10.3 1.0
OD1 A:ASN41 4.3 12.3 1.0
CB G:GLU42 4.4 13.8 1.0
CG G:GLU43 4.4 13.0 1.0
N G:GLU43 4.4 11.0 1.0
CB G:GLU43 4.8 11.9 1.0
CA G:GLU42 4.8 11.7 1.0

Zinc binding site 4 out of 13 in 7v1q

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Zinc binding site 4 out of 13 in the Leifsonia Alcohol Dehydrogenases Lnadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Leifsonia Alcohol Dehydrogenases Lnadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:11.8
occ:1.00
 O D:HOH455 2.1 16.4 1.0
O B:GLN251 2.1 5.7 0.5
O B:HOH419 2.1 10.8 1.0
O B:HOH523 2.1 13.3 1.0
O D:GLN251 2.1 5.8 0.5
O D:HOH411 2.1 9.5 1.0
C B:GLN251 3.0 9.8 0.5
C D:GLN251 3.1 9.7 0.5
C D:GLN251 3.1 9.8 0.5
C B:GLN251 3.1 10.4 0.5
O D:GLN251 3.3 6.6 0.5
O B:GLN251 3.4 6.8 0.5
O D:HOH468 4.2 17.7 1.0
O B:HOH527 4.2 18.5 1.0
O B:HOH441 4.4 18.3 1.0
O D:TYR248 4.4 9.2 1.0
CA D:GLN251 4.4 10.7 0.5
CA B:GLN251 4.5 10.9 0.5
CA D:GLN251 4.5 10.5 0.5
O B:TYR248 4.5 7.3 1.0
CA B:GLN251 4.5 11.3 0.5
CG1 D:VAL149 4.7 7.8 1.0
O D:THR249 4.7 10.7 1.0
O B:THR249 4.7 10.7 1.0
CG1 B:VAL149 4.7 6.6 1.0
N D:GLN251 4.7 10.4 0.5
N B:GLN251 4.7 10.8 0.5
N B:GLN251 4.7 10.7 0.5
N D:GLN251 4.7 10.3 0.5
CA D:THR249 4.8 8.5 1.0
CA B:THR249 4.9 8.1 1.0
CG D:GLN251 4.9 13.3 0.5
CG B:GLN251 4.9 13.8 0.5
C D:THR249 4.9 9.1 1.0
C B:THR249 5.0 8.9 1.0
CG D:GLN251 5.0 13.8 0.5
CG B:GLN251 5.0 14.4 0.5

Zinc binding site 5 out of 13 in 7v1q

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Zinc binding site 5 out of 13 in the Leifsonia Alcohol Dehydrogenases Lnadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Leifsonia Alcohol Dehydrogenases Lnadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:16.4
occ:1.00
 O B:HOH518 2.0 13.0 1.0
OE1 B:GLU43 2.0 11.9 1.0
O B:HOH446 2.1 10.2 1.0
O B:HOH436 2.2 14.2 1.0
CD B:GLU43 2.9 13.7 1.0
OE2 B:GLU43 3.2 16.8 1.0
O B:HOH543 4.0 18.7 1.0
ND2 B:ASN41 4.3 10.4 1.0
N B:GLU42 4.3 10.8 1.0
CG B:GLU43 4.4 12.6 1.0
N B:GLU43 4.4 10.5 1.0
CB B:GLU42 4.4 13.1 1.0
CB B:GLU43 4.8 11.6 1.0
CA B:GLU42 4.9 11.5 1.0

Zinc binding site 6 out of 13 in 7v1q

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Zinc binding site 6 out of 13 in the Leifsonia Alcohol Dehydrogenases Lnadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Leifsonia Alcohol Dehydrogenases Lnadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:16.6
occ:1.00
 O B:HOH502 2.1 13.3 1.0
NE2 B:HIS44 2.1 12.6 1.0
O B:HOH490 2.2 11.6 1.0
O B:HOH531 2.4 20.1 1.0
CE1 B:HIS44 3.0 12.5 1.0
CD2 B:HIS44 3.2 12.2 1.0
ND1 B:HIS44 4.1 12.5 1.0
OD1 B:ASN41 4.2 11.6 1.0
CG B:HIS44 4.3 11.4 1.0

Zinc binding site 7 out of 13 in 7v1q

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Zinc binding site 7 out of 13 in the Leifsonia Alcohol Dehydrogenases Lnadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Leifsonia Alcohol Dehydrogenases Lnadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn306

b:23.0
occ:1.00
 O B:HOH483 2.0 21.0 1.0
O B:HOH514 2.1 20.8 1.0
O B:HOH424 2.1 25.1 1.0
OE2 B:GLU196 2.2 21.3 1.0
O B:HOH413 2.2 17.0 1.0
CD B:GLU196 3.0 23.6 1.0
OE1 B:GLU196 3.2 25.3 1.0
NE B:ARG191 4.0 21.0 1.0
OE1 B:GLU218 4.1 13.7 1.0
OE2 B:GLU218 4.3 15.3 1.0
O B:ARG191 4.4 13.2 1.0
CB B:ARG191 4.4 13.7 1.0
CG B:GLU196 4.4 21.3 1.0
NH2 B:ARG191 4.4 26.1 1.0
O B:HOH532 4.6 24.2 1.0
CD B:GLU218 4.6 12.8 1.0
CZ B:ARG191 4.7 23.0 1.0
CD B:ARG191 4.8 18.4 1.0

Zinc binding site 8 out of 13 in 7v1q

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Zinc binding site 8 out of 13 in the Leifsonia Alcohol Dehydrogenases Lnadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Leifsonia Alcohol Dehydrogenases Lnadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:11.7
occ:1.00
 O G:HOH430 2.1 10.7 1.0
O G:HOH493 2.1 16.3 1.0
O G:GLN251 2.1 6.8 0.5
O C:HOH465 2.1 13.2 1.0
O C:GLN251 2.1 6.3 0.5
O C:HOH407 2.2 9.5 1.0
C G:GLN251 3.1 10.2 0.5
C C:GLN251 3.1 9.9 0.5
C G:GLN251 3.1 10.4 0.5
C C:GLN251 3.1 10.1 0.5
O C:GLN251 3.3 5.6 0.5
O G:GLN251 3.4 6.6 0.5
O C:HOH469 4.2 19.5 1.0
O G:HOH500 4.2 20.6 1.0
O G:HOH419 4.4 19.5 1.0
CA G:GLN251 4.4 11.0 0.5
O C:TYR248 4.4 8.3 1.0
CA G:GLN251 4.4 11.4 0.5
O G:TYR248 4.4 7.5 1.0
CA C:GLN251 4.5 10.8 0.5
CA C:GLN251 4.5 10.7 0.5
O C:THR249 4.7 10.9 1.0
N G:GLN251 4.7 11.1 0.5
N G:GLN251 4.7 10.8 0.5
O G:THR249 4.7 10.3 1.0
CG1 C:VAL149 4.7 7.5 1.0
CG1 G:VAL149 4.7 6.6 1.0
N C:GLN251 4.7 10.3 0.5
N C:GLN251 4.7 10.3 0.5
CG G:GLN251 4.8 13.0 0.5
CA G:THR249 4.9 7.8 1.0
CG C:GLN251 4.9 13.2 0.5
CA C:THR249 4.9 8.6 1.0
CG G:GLN251 4.9 14.7 0.5
CG C:GLN251 4.9 13.6 0.5
C C:THR249 4.9 9.1 1.0
C G:THR249 5.0 8.8 1.0

Zinc binding site 9 out of 13 in 7v1q

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Zinc binding site 9 out of 13 in the Leifsonia Alcohol Dehydrogenases Lnadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Leifsonia Alcohol Dehydrogenases Lnadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn304

b:17.1
occ:1.00
 O C:HOH461 2.0 19.6 1.0
OE1 C:GLU43 2.1 13.1 1.0
O C:HOH444 2.2 20.1 1.0
O C:HOH472 2.4 19.2 1.0
CD C:GLU43 3.0 16.1 1.0
OE2 C:GLU43 3.2 19.6 1.0
O C:HOH475 4.1 22.2 1.0
ND2 C:ASN41 4.3 11.1 1.0
N C:GLU42 4.4 12.8 1.0
CG C:GLU43 4.4 14.8 1.0
N C:GLU43 4.5 13.4 1.0
CB C:GLU42 4.6 14.3 1.0
CB C:GLU43 4.8 14.4 1.0
CA C:GLU42 5.0 13.6 1.0

Zinc binding site 10 out of 13 in 7v1q

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Zinc binding site 10 out of 13 in the Leifsonia Alcohol Dehydrogenases Lnadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Leifsonia Alcohol Dehydrogenases Lnadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn305

b:17.4
occ:1.00
 O C:HOH476 2.0 19.6 1.0
CE1 C:HIS44 2.1 14.4 1.0
O C:HOH462 2.2 18.4 1.0
O C:HOH487 2.3 19.2 1.0
NE2 C:HIS44 2.9 14.6 1.0
ND1 C:HIS44 3.2 15.3 1.0
CD2 C:HIS44 4.1 13.0 1.0
CG C:HIS44 4.3 13.7 1.0
OD1 C:ASN41 4.4 13.8 1.0

Reference:

L.Zhu, Y.Song, C.Chang, H.Ma, L.Yang, Z.Deng, W.Deng, X.Qu. Engineering Leifsonia Alcohol Dehydrogenase For Thermostability and Catalytic Efficiency By Enhancing Subunit Interactions. Chembiochem V. 22 3178 2021.
ISSN: ESSN 1439-7633
PubMed: 34549865
DOI: 10.1002/CBIC.202100431
Page generated: Wed Oct 30 12:28:28 2024

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