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Zinc in PDB 3meq: Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis

Protein crystallography data

The structure of Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis, PDB code: 3meq was solved by T.L.Arakaki, B.L.Staker, A.Gardberg, Seattle Structural Genomics Centerfor Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.75 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.365, 103.799, 152.390, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.4

Other elements in 3meq:

The structure of Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis (pdb code 3meq). 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 Alcohol Dehydrogenase From Brucella Melitensis, PDB code: 3meq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3meq

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Zinc binding site 1 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis


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 Alcohol Dehydrogenase From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:30.8
occ:1.00
 O2 A:EDO402 2.1 30.4 1.0
NE2 A:HIS65 2.1 26.9 1.0
SG A:CYS152 2.3 29.2 1.0
SG A:CYS42 2.4 32.0 1.0
CD2 A:HIS65 2.8 26.1 1.0
C2 A:EDO402 3.0 34.8 1.0
C5N A:NAI601 3.2 34.3 1.0
CE1 A:HIS65 3.2 28.0 1.0
CB A:CYS152 3.3 26.9 1.0
CB A:CYS42 3.3 31.1 1.0
C6N A:NAI601 3.9 33.7 1.0
OG1 A:THR44 4.0 30.9 1.0
C4N A:NAI601 4.0 34.0 1.0
CB A:THR44 4.0 29.2 1.0
CG A:HIS65 4.1 26.4 1.0
ND1 A:HIS65 4.2 23.6 1.0
C1 A:EDO402 4.3 34.8 1.0
CA A:CYS152 4.6 25.9 1.0
NH2 A:ARG337 4.7 32.4 1.0
CG2 A:THR44 4.8 26.5 1.0
CA A:CYS42 4.8 31.2 1.0
OE2 A:GLU66 4.9 29.4 1.0
O1 A:EDO402 4.9 39.8 1.0
N A:THR44 5.0 29.5 1.0
N1N A:NAI601 5.0 32.2 1.0
C A:CYS152 5.0 26.3 1.0

Zinc binding site 2 out of 8 in 3meq

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Zinc binding site 2 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis


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 Alcohol Dehydrogenase From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:22.6
occ:1.00
 SG A:CYS99 2.3 25.8 1.0
SG A:CYS96 2.3 26.4 1.0
SG A:CYS110 2.3 25.4 1.0
SG A:CYS102 2.4 25.3 1.0
CB A:CYS110 3.2 25.0 1.0
CB A:CYS99 3.4 26.4 1.0
CB A:CYS102 3.4 25.7 1.0
CB A:CYS96 3.4 26.6 1.0
N A:CYS96 3.6 25.8 1.0
N A:GLY97 3.9 26.3 1.0
CA A:CYS96 3.9 26.3 1.0
N A:CYS99 3.9 26.9 1.0
CA A:CYS110 4.0 25.1 1.0
O A:HOH361 4.2 22.2 1.0
CA A:CYS99 4.2 26.8 1.0
N A:CYS102 4.2 25.5 1.0
C A:CYS96 4.3 26.6 1.0
CA A:CYS102 4.4 25.6 1.0
N A:HIS98 4.5 27.2 1.0
C A:ALA95 4.7 25.6 1.0
CB A:ALA95 4.8 24.9 1.0
C A:CYS99 4.9 26.6 1.0
CA A:GLY97 4.9 26.7 1.0
C A:CYS110 4.9 25.4 1.0
O A:CYS99 4.9 26.6 1.0

Zinc binding site 3 out of 8 in 3meq

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Zinc binding site 3 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis


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 Alcohol Dehydrogenase From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:47.5
occ:1.00
 O2 B:EDO402 2.2 40.5 1.0
NE2 B:HIS65 2.2 32.2 1.0
SG B:CYS152 2.3 36.6 1.0
SG B:CYS42 2.3 26.0 0.5
SG B:CYS42 2.5 28.7 0.5
CD2 B:HIS65 3.0 28.7 1.0
C2 B:EDO402 3.2 42.9 1.0
CB B:CYS42 3.2 31.9 0.5
CB B:CYS152 3.3 28.4 1.0
CB B:CYS42 3.3 32.5 0.5
CE1 B:HIS65 3.3 31.3 1.0
OG1 B:THR44 4.0 32.5 1.0
CB B:THR44 4.1 31.7 1.0
CG B:HIS65 4.2 26.9 1.0
ND1 B:HIS65 4.4 28.8 1.0
C1 B:EDO402 4.5 45.3 1.0
CA B:CYS152 4.7 26.9 1.0
CA B:CYS42 4.7 33.5 0.5
CA B:CYS42 4.8 33.9 0.5
O1 B:EDO402 4.8 51.2 1.0
CG2 B:THR44 4.9 29.1 1.0

Zinc binding site 4 out of 8 in 3meq

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Zinc binding site 4 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis


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 Alcohol Dehydrogenase From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:23.2
occ:1.00
 SG B:CYS110 2.3 26.0 1.0
SG B:CYS99 2.3 26.4 1.0
SG B:CYS96 2.3 26.9 1.0
SG B:CYS102 2.4 25.7 1.0
CB B:CYS110 3.2 25.6 1.0
CB B:CYS96 3.4 27.0 1.0
CB B:CYS99 3.4 27.0 1.0
CB B:CYS102 3.5 26.1 1.0
N B:CYS96 3.5 26.2 1.0
CA B:CYS96 3.9 26.7 1.0
N B:CYS99 3.9 27.3 1.0
N B:GLY97 3.9 26.6 1.0
CA B:CYS110 4.0 25.9 1.0
O B:HOH385 4.1 24.2 1.0
CA B:CYS99 4.2 27.3 1.0
N B:CYS102 4.2 26.0 1.0
C B:CYS96 4.3 26.9 1.0
CA B:CYS102 4.4 26.0 1.0
N B:HIS98 4.6 27.5 1.0
C B:ALA95 4.6 25.9 1.0
CB B:ALA95 4.7 25.3 1.0
C B:CYS99 4.9 27.2 1.0
C B:CYS110 4.9 26.3 1.0
CA B:GLY97 4.9 26.9 1.0
O B:CYS99 4.9 27.0 1.0
N B:GLU111 5.0 26.7 1.0

Zinc binding site 5 out of 8 in 3meq

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Zinc binding site 5 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis


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 Alcohol Dehydrogenase From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:51.2
occ:1.00
 O1 C:EDO402 2.2 21.2 0.5
SG C:CYS152 2.3 39.7 1.0
NE2 C:HIS65 2.3 37.4 1.0
SG C:CYS42 2.5 37.3 0.5
SG C:CYS42 2.6 34.8 0.5
C1 C:EDO402 2.9 24.2 0.5
CB C:CYS42 3.2 39.4 0.5
CD2 C:HIS65 3.2 35.6 1.0
CB C:CYS42 3.3 39.8 0.5
CB C:CYS152 3.3 32.2 1.0
CE1 C:HIS65 3.4 38.7 1.0
OG1 C:THR44 4.0 38.7 1.0
CB C:THR44 4.1 40.0 1.0
C2 C:EDO402 4.3 26.4 0.5
CG C:HIS65 4.4 36.1 1.0
ND1 C:HIS65 4.5 36.4 1.0
CA C:CYS42 4.7 41.3 0.5
O2 C:EDO402 4.7 30.1 0.5
CA C:CYS152 4.7 31.3 1.0
CA C:CYS42 4.8 41.7 0.5
NH2 C:ARG337 4.8 48.0 1.0
CG2 C:THR44 4.9 37.3 1.0

Zinc binding site 6 out of 8 in 3meq

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Zinc binding site 6 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis


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 Alcohol Dehydrogenase From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:30.6
occ:1.00
 SG C:CYS102 2.3 29.3 1.0
SG C:CYS110 2.3 30.9 1.0
SG C:CYS96 2.4 35.7 1.0
SG C:CYS99 2.4 30.1 1.0
CB C:CYS110 3.3 31.9 1.0
CB C:CYS99 3.4 31.6 1.0
CB C:CYS102 3.4 29.6 1.0
CB C:CYS96 3.5 37.1 1.0
N C:CYS96 3.5 36.0 1.0
N C:GLY97 3.8 35.6 1.0
N C:CYS99 3.9 33.2 1.0
CA C:CYS96 3.9 36.8 1.0
CA C:CYS110 4.0 31.5 1.0
CA C:CYS99 4.2 32.1 1.0
N C:CYS102 4.2 29.9 1.0
O C:HOH378 4.3 31.5 1.0
C C:CYS96 4.3 36.8 1.0
CA C:CYS102 4.4 29.4 1.0
N C:HIS98 4.5 35.7 1.0
C C:ALA95 4.6 36.0 1.0
CB C:ALA95 4.7 34.5 1.0
CA C:GLY97 4.8 36.0 1.0
C C:CYS99 4.8 32.0 1.0
C C:CYS110 4.9 33.0 1.0
O C:CYS99 4.9 30.7 1.0

Zinc binding site 7 out of 8 in 3meq

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Zinc binding site 7 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis


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 Alcohol Dehydrogenase From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:48.6
occ:1.00
 O2 D:EDO402 2.1 38.5 1.0
NE2 D:HIS65 2.2 34.0 1.0
SG D:CYS152 2.3 39.6 1.0
SG D:CYS42 2.4 29.1 0.5
SG D:CYS42 2.5 28.4 0.5
C2 D:EDO402 2.9 39.8 1.0
CD2 D:HIS65 3.1 31.2 1.0
CB D:CYS42 3.2 33.1 0.5
CE1 D:HIS65 3.2 33.2 1.0
CB D:CYS42 3.3 33.8 0.5
CB D:CYS152 3.4 31.4 1.0
OG1 D:THR44 3.9 31.8 1.0
CB D:THR44 3.9 31.7 1.0
CG D:HIS65 4.3 29.5 1.0
C1 D:EDO402 4.3 43.5 1.0
ND1 D:HIS65 4.3 29.4 1.0
CG2 D:THR44 4.6 30.3 1.0
CA D:CYS42 4.8 34.7 0.5
CA D:CYS152 4.8 30.1 1.0
CA D:CYS42 4.8 35.0 0.5
O1 D:EDO402 4.9 46.5 1.0
NH2 D:ARG337 4.9 44.1 1.0

Zinc binding site 8 out of 8 in 3meq

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Zinc binding site 8 out of 8 in the Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis


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 Alcohol Dehydrogenase From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:30.2
occ:1.00
 SG D:CYS102 2.3 29.9 1.0
SG D:CYS110 2.3 30.7 1.0
SG D:CYS96 2.4 32.0 1.0
SG D:CYS99 2.4 29.7 1.0
CB D:CYS110 3.2 28.1 1.0
CB D:CYS102 3.4 30.8 1.0
CB D:CYS96 3.4 34.0 1.0
CB D:CYS99 3.4 30.2 1.0
N D:CYS96 3.5 33.1 1.0
N D:GLY97 3.8 32.6 1.0
CA D:CYS96 3.9 33.5 1.0
N D:CYS99 3.9 31.9 1.0
CA D:CYS110 4.0 27.9 1.0
O D:HOH409 4.2 30.8 1.0
N D:CYS102 4.2 29.9 1.0
CA D:CYS99 4.3 31.1 1.0
C D:CYS96 4.3 33.7 1.0
CA D:CYS102 4.4 29.6 1.0
N D:HIS98 4.5 33.5 1.0
C D:ALA95 4.6 33.1 1.0
CB D:ALA95 4.7 30.8 1.0
CA D:GLY97 4.8 33.1 1.0
C D:CYS110 4.9 28.6 1.0
C D:CYS99 4.9 30.8 1.0
O D:CYS99 5.0 29.7 1.0
N D:GLU111 5.0 29.9 1.0

Reference:

T.L.Arakaki, A.Gardberg, B.L.Staker, B.Sankaran. Crystal Structure of Alcohol Dehydrogenase From Brucella Melitensis To Be Published.
Page generated: Sat Oct 26 09:26:35 2024

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