Zinc in PDB 7lm5: Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae

Protein crystallography data

The structure of Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae, PDB code: 7lm5 was solved by Z.Luo, M.Zupan, C.A.Mcdevitt, B.Kobe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.16 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 46.229, 71.979, 81.914, 90, 95.45, 90
R / Rfree (%) 22.5 / 26.9

Other elements in 7lm5:

The structure of Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae also contains other interesting chemical elements:

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

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae (pdb code 7lm5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae, PDB code: 7lm5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 7lm5

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Zinc binding site 1 out of 11 in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae


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 the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:37.6
occ:0.97
OE2 A:GLU280 1.9 34.3 1.0
NE2 A:HIS141 1.9 30.0 1.0
NE2 A:HIS205 2.5 35.7 1.0
CE1 A:HIS141 2.9 30.0 1.0
CD A:GLU280 2.9 35.7 1.0
CD2 A:HIS141 2.9 30.0 1.0
CL A:CL412 3.1 54.0 1.0
CD2 A:HIS205 3.2 36.4 1.0
O A:ILE225 3.3 47.3 1.0
OE1 A:GLU280 3.3 36.3 1.0
CE1 A:HIS205 3.7 36.0 1.0
ND1 A:HIS141 4.0 30.0 1.0
CG A:HIS141 4.1 30.0 1.0
CB A:ALA207 4.1 33.0 1.0
CG A:GLU280 4.3 37.0 1.0
CG A:HIS205 4.4 37.4 1.0
C A:ILE225 4.5 47.7 1.0
CD A:PRO227 4.6 48.8 1.0
ND1 A:HIS205 4.6 36.9 1.0
CA A:ALA207 4.8 31.0 1.0
CG A:PRO227 4.9 45.3 1.0
O A:THR206 5.0 26.3 1.0

Zinc binding site 2 out of 11 in 7lm5

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Zinc binding site 2 out of 11 in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae


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 the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:46.8
occ:0.50
O A:HOH552 2.2 44.0 1.0
NE2 A:HIS167 2.2 50.9 1.0
O A:HOH560 2.9 42.1 0.5
CD2 A:HIS167 3.0 51.5 1.0
CE1 A:HIS167 3.1 49.1 1.0
CG A:HIS167 4.1 50.1 1.0
ND1 A:HIS167 4.1 48.6 1.0
CD2 A:LEU52 4.6 42.0 1.0

Zinc binding site 3 out of 11 in 7lm5

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Zinc binding site 3 out of 11 in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae


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 the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:53.3
occ:1.00
OD2 A:ASP164 2.1 46.7 1.0
ND1 A:HIS167 2.2 48.6 1.0
OD1 A:ASP164 2.3 52.2 1.0
CG A:ASP164 2.4 48.5 1.0
CE1 A:HIS167 2.8 49.1 1.0
CG A:HIS167 3.3 50.1 1.0
CB A:ASP164 3.9 46.9 1.0
CB A:HIS167 3.9 50.1 1.0
NE2 A:HIS167 3.9 50.9 1.0
OH A:TYR171 3.9 37.4 1.0
CD2 A:HIS167 4.2 51.5 1.0
OD1 A:ASN53 4.3 42.1 1.0
N A:HIS167 4.7 50.6 1.0
CA A:ASP164 4.9 50.7 1.0
CZ A:TYR171 5.0 37.5 1.0
O A:ASP164 5.0 50.4 1.0
CA A:HIS167 5.0 51.2 1.0

Zinc binding site 4 out of 11 in 7lm5

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Zinc binding site 4 out of 11 in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae


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 the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:49.6
occ:0.62
O A:HOH530 2.1 44.0 1.0
O A:HOH539 2.1 44.0 1.0
OE2 A:GLU110 2.2 42.6 1.0
ND1 A:HIS88 2.2 40.7 1.0
OE1 A:GLU110 2.4 45.5 1.0
CD A:GLU110 2.6 44.1 1.0
CE1 A:HIS88 3.0 39.2 1.0
CG A:HIS88 3.3 42.0 1.0
CB A:HIS88 3.8 44.4 1.0
NE2 A:HIS88 4.1 39.2 1.0
CG A:GLU110 4.1 44.1 1.0
N A:HIS88 4.2 41.4 1.0
CD2 A:HIS88 4.3 40.9 1.0
O A:HOH551 4.3 42.1 1.0
O A:HOH504 4.6 40.3 1.0
CA A:HIS88 4.6 43.4 1.0
OH A:TYR85 4.7 39.5 1.0
CB A:GLU110 5.0 46.4 1.0

Zinc binding site 5 out of 11 in 7lm5

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Zinc binding site 5 out of 11 in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae


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 the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:62.2
occ:0.91
OE1 A:GLU118 2.5 48.8 1.0
OE2 A:GLU118 2.9 48.7 1.0
CD A:GLU118 3.0 48.0 1.0
CG A:GLU118 4.5 46.2 1.0

Zinc binding site 6 out of 11 in 7lm5

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Zinc binding site 6 out of 11 in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae


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 the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:72.5
occ:0.95
OE2 A:GLU127 2.0 64.3 1.0
CD A:GLU127 2.9 62.7 1.0
OE1 A:GLU127 3.1 63.4 1.0
CG A:GLU127 4.3 60.2 1.0

Zinc binding site 7 out of 11 in 7lm5

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Zinc binding site 7 out of 11 in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae


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 the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:59.7
occ:0.77
OE2 A:GLU302 2.1 60.7 1.0
CD A:GLU302 2.8 59.9 1.0
OE1 A:GLU302 2.9 60.8 1.0
CG A:GLU302 4.3 58.0 1.0

Zinc binding site 8 out of 11 in 7lm5

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Zinc binding site 8 out of 11 in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae


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 the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:38.6
occ:0.42
OE2 A:GLU294 2.2 48.0 1.0
CD A:GLU294 2.9 47.4 1.0
OE1 A:GLU294 3.0 47.7 1.0
NZ A:LYS188 4.2 50.5 1.0
O A:HOH559 4.3 40.5 1.0
CG A:GLU294 4.4 46.8 1.0
CB A:GLU294 5.0 46.8 1.0

Zinc binding site 9 out of 11 in 7lm5

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Zinc binding site 9 out of 11 in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:38.6
occ:0.31
O A:HOH509 2.1 41.2 1.0
O A:HOH502 2.2 44.0 1.0
OE2 A:GLU291 2.7 59.6 1.0
OE1 A:GLU291 3.1 58.4 1.0
CD A:GLU291 3.3 58.1 1.0
O A:ASP286 4.3 87.9 1.0
CG A:GLU291 4.8 55.9 1.0
CA A:LYS287 4.8 66.4 1.0
CG2 A:THR288 5.0 48.7 1.0

Zinc binding site 10 out of 11 in 7lm5

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Zinc binding site 10 out of 11 in the Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Zn(II)-Bound Adcaii H65A Mutant Variant of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn410

b:38.6
occ:0.24
OE1 A:GLU184 2.3 64.2 1.0
NZ A:LYS180 2.9 53.3 1.0
CD A:GLU184 3.1 64.6 1.0
CE A:LYS180 3.2 53.1 1.0
OE2 A:GLU184 3.2 65.5 1.0
CD A:LYS180 4.1 55.8 1.0
CG A:LYS181 4.4 58.4 1.0
CG A:GLU184 4.5 64.0 1.0
CB A:GLU184 5.0 61.5 1.0

Reference:

M.L.Zupan, Z.Luo, K.Ganio, V.G.Pederick, S.L.Neville, E.Deplazes, B.Kobe, C.A.Mcdevitt. Conformation of the Solute-Binding Protein Adcaii Influences Zinc Uptake in Streptococcus Pneumoniae . Front Cell Infect Microbiol V. 11 29981 2021.
ISSN: ESSN 2235-2988
PubMed: 34490149
DOI: 10.3389/FCIMB.2021.729981
Page generated: Fri Nov 5 16:54:08 2021

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