Zinc in PDB 7lm6: Crystal Structure of the Zn(II)-Bound Adcaii H205L Mutant Variant of Streptococcus Pneumoniae

The structure of Crystal Structure of the Zn(II)-Bound Adcaii H205L Mutant Variant of Streptococcus Pneumoniae, PDB code: 7lm6 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)	49.62 / 3.37
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	119.792, 119.792, 169.503, 90, 90, 120
R / Rfree (%)	22.9 / 24.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Zn(II)-Bound Adcaii H205L Mutant Variant of Streptococcus Pneumoniae (pdb code 7lm6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of the Zn(II)-Bound Adcaii H205L Mutant Variant of Streptococcus Pneumoniae, PDB code: 7lm6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of the Zn(II)-Bound Adcaii H205L 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 H205L Mutant Variant of Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:154.6 occ:0.70 OD2 A:ASP81 3.5 111.7 1.0 OD1 A:ASP81 4.2 116.9 1.0 CG A:ASP81 4.2 108.6 1.0 O A:GLY31 4.4 95.9 1.0 HA A:MET32 4.6 88.5 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of the Zn(II)-Bound Adcaii H205L 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 H205L Mutant Variant of Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:58.4 occ:1.00 NE2 A:HIS141 2.1 51.6 1.0 OE2 A:GLU280 2.4 40.5 1.0 ND1 A:HIS65 2.4 81.7 1.0 CD A:GLU280 2.7 55.5 1.0 OE1 A:GLU280 2.7 81.6 1.0 CE1 A:HIS141 3.0 64.3 1.0 HE1 A:HIS141 3.1 65.5 1.0 CE1 A:HIS65 3.2 81.7 1.0 CD2 A:HIS141 3.2 54.8 1.0 HD2 A:HIS141 3.4 55.9 1.0 CG A:HIS65 3.6 81.7 1.0 HB2 A:ALA207 3.9 48.1 1.0 CG A:GLU280 3.9 50.6 1.0 HG3 A:GLU280 4.1 48.2 1.0 HG2 A:GLU280 4.1 48.2 1.0 CB A:HIS65 4.1 81.7 1.0 ND1 A:HIS141 4.2 54.6 1.0 HB1 A:ALA207 4.2 48.1 1.0 CG A:HIS141 4.3 50.3 1.0 NE2 A:HIS65 4.4 81.7 1.0 HH2 A:TRP143 4.5 50.6 1.0 CB A:ALA207 4.5 50.3 1.0 CD2 A:HIS65 4.6 81.7 1.0 HB2 A:PRO278 4.7 46.5 1.0 HZ2 A:TRP143 4.8 50.8 1.0 HD11 A:LEU205 4.9 53.6 1.0 HD1 A:HIS141 4.9 55.8 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of the Zn(II)-Bound Adcaii H205L 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 H205L Mutant Variant of Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:86.3 occ:1.00 OE1 A:GLU151 2.4 49.0 1.0 HE2 A:LYS148 2.7 86.3 1.0 H A:THR116 3.1 77.9 1.0 CD A:GLU151 3.1 77.3 1.0 HB A:THR116 3.4 81.8 1.0 OE2 A:GLU151 3.4 80.0 1.0 HE3 A:LYS148 3.5 86.3 1.0 HE3 A:MET115 3.5 67.0 1.0 HG1 A:THR116 3.5 88.7 1.0 CE A:LYS148 3.5 82.7 1.0 OG1 A:THR116 3.6 83.8 1.0 N A:THR116 3.9 72.9 1.0 HA A:MET115 3.9 65.8 1.0 CB A:THR116 4.0 76.8 1.0 HZ1 A:LYS148 4.0 79.5 1.0 HE2 A:MET115 4.1 67.0 1.0 CE A:MET115 4.2 62.4 1.0 HG2 A:GLU151 4.3 76.5 1.0 NZ A:LYS148 4.3 76.0 1.0 CG A:GLU151 4.3 69.6 1.0 HB3 A:MET115 4.4 63.5 1.0 HD2 A:LYS148 4.5 70.5 1.0 CA A:THR116 4.5 67.1 1.0 CD A:LYS148 4.6 66.9 1.0 HG2 A:MET115 4.6 67.8 1.0 CA A:MET115 4.6 61.1 1.0 HZ3 A:LYS148 4.7 79.5 1.0 HE1 A:MET115 4.7 67.0 1.0 HG3 A:LYS148 4.7 55.2 1.0 C A:MET115 4.8 64.2 1.0 HB3 A:GLU151 4.8 60.4 1.0 CB A:MET115 4.9 58.9 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of the Zn(II)-Bound Adcaii H205L 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 H205L Mutant Variant of Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:92.8 occ:0.98 OD2 A:ASP164 2.0 74.5 1.0 ND1 A:HIS167 2.1 76.0 1.0 OD1 A:ASP164 2.5 89.7 1.0 CG A:ASP164 2.5 83.5 1.0 CE1 A:HIS167 2.9 85.7 1.0 HB2 A:HIS167 3.0 80.7 1.0 HE1 A:HIS167 3.1 79.0 1.0 CG A:HIS167 3.1 84.8 1.0 HB2 A:GLU166 3.4 79.3 1.0 CB A:HIS167 3.5 87.4 1.0 NE2 A:HIS167 3.9 87.3 1.0 H A:HIS167 4.0 94.0 1.0 CB A:ASP164 4.0 83.7 1.0 CD2 A:HIS167 4.0 81.9 1.0 HD13 A:LEU52 4.2 82.0 1.0 HB3 A:ASP164 4.2 76.4 1.0 HB3 A:HIS167 4.2 80.7 1.0 OH A:TYR171 4.3 79.5 1.0 N A:HIS167 4.3 100.7 1.0 HH A:TYR171 4.3 76.4 1.0 HB2 A:ASP164 4.3 76.4 1.0 CB A:GLU166 4.4 84.5 1.0 HB3 A:LEU52 4.5 80.2 1.0 CA A:HIS167 4.6 93.4 1.0 OE1 A:GLU166 4.6 110.4 1.0 HE2 A:HIS167 4.7 80.6 1.0 HB3 A:GLU166 4.7 79.3 1.0 HD2 A:HIS167 4.9 75.2 1.0 HA A:ASP164 4.9 73.6 1.0 O A:ASP164 4.9 87.5 1.0 CA A:ASP164 4.9 80.9 1.0 C A:GLU166 5.0 96.8 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of the Zn(II)-Bound Adcaii H205L 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 H205L Mutant Variant of Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:87.5 occ:1.00 HD1 A:HIS88 1.8 67.7 1.0 OE2 A:GLU110 2.0 71.3 1.0 ND1 A:HIS88 2.1 70.1 1.0 OE1 A:GLU110 2.6 75.4 1.0 CD A:GLU110 2.6 71.3 1.0 CE1 A:HIS88 2.8 67.2 1.0 CG A:HIS88 2.9 75.7 1.0 HB3 A:HIS88 3.0 71.0 1.0 HE1 A:HIS88 3.0 64.8 1.0 H A:HIS88 3.3 70.9 1.0 CB A:HIS88 3.5 73.5 1.0 NE2 A:HIS88 3.7 83.7 1.0 CD2 A:HIS88 3.7 71.0 1.0 N A:HIS88 4.0 73.4 1.0 CG A:GLU110 4.1 64.6 1.0 HB2 A:HIS88 4.2 71.0 1.0 HH A:TYR85 4.3 67.2 1.0 HG2 A:GLU110 4.4 66.0 1.0 CA A:HIS88 4.4 73.7 1.0 HG A:SER87 4.4 62.3 1.0 HG3 A:GLU110 4.5 66.0 1.0 HD2 A:HIS88 4.5 68.6 1.0 HA A:GLU113 4.5 73.7 1.0 HG3 A:GLU113 4.6 84.3 1.0 HA A:SER87 4.7 64.2 1.0 OG A:SER87 4.8 60.9 1.0 OH A:TYR85 4.9 70.6 1.0 HB2 A:GLU110 5.0 63.9 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of the Zn(II)-Bound Adcaii H205L 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 H205L Mutant Variant of Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:122.0 occ:0.99 OE1 A:GLU294 2.1 79.7 1.0 CD A:GLU294 2.8 89.0 1.0 OE2 A:GLU294 2.8 99.0 1.0 HZ3 A:LYS188 3.2 69.7 1.0 HZ2 A:LYS188 3.9 69.7 1.0 NZ A:LYS188 3.9 70.6 1.0 CG A:GLU294 4.2 66.7 1.0 HZ1 A:LYS188 4.3 69.7 1.0 HG2 A:GLU291 4.4 74.3 1.0 HB2 A:GLU294 4.5 69.0 1.0 HD3 A:LYS188 4.5 60.5 1.0 HG A:LEU185 4.6 62.2 1.0 HG3 A:GLU294 4.6 71.1 1.0 HB3 A:GLU294 4.8 69.0 1.0 HG2 A:GLU294 4.8 71.1 1.0 CB A:GLU294 4.8 64.5 1.0 HA A:GLU291 5.0 63.3 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of the Zn(II)-Bound Adcaii H205L 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 H205L Mutant Variant of Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:128.3 occ:1.00 OE2 A:GLU147 2.9 101.2 1.0 CD A:GLU147 3.8 99.6 1.0 HE22 A:GLN183 4.0 109.7 1.0 OE1 A:GLU147 4.0 99.9 1.0 HG21 A:THR186 4.1 70.2 1.0 HH21 A:ARG214 4.3 68.0 1.0 HG22 A:THR186 4.5 70.2 1.0 NH2 A:ARG214 4.6 67.8 1.0 NE2 A:GLN183 4.6 106.5 1.0 HE A:ARG214 4.6 60.7 1.0 OE1 A:GLN190 4.6 107.3 1.0 HE21 A:GLN183 4.7 109.7 1.0 CG2 A:THR186 4.8 67.1 1.0 NE A:ARG214 4.9 60.5 1.0 CZ A:ARG214 4.9 59.8 1.0 HH22 A:ARG214 4.9 68.0 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of the Zn(II)-Bound Adcaii H205L 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 H205L Mutant Variant of Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:131.1 occ:0.89 OE2 A:GLU295 2.7 106.5 1.0 OE1 A:GLU295 2.7 117.3 1.0 CD A:GLU295 3.1 117.7 1.0 HZ1 A:LYS287 3.5 114.1 1.0 HD22 A:ASN285 3.8 76.4 1.0 HE2 A:LYS287 4.0 100.1 1.0 NZ A:LYS287 4.3 111.2 1.0 HE3 A:LYS287 4.3 100.1 1.0 HD21 A:ASN285 4.3 76.4 1.0 ND2 A:ASN285 4.4 77.4 1.0 CE A:LYS287 4.4 97.1 1.0 CG A:GLU295 4.5 101.8 1.0 HZ2 A:LYS287 4.6 114.1 1.0 HG2 A:GLU295 4.8 103.1 1.0 HZ3 A:LYS287 4.9 114.1 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of the Zn(II)-Bound Adcaii H205L 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 H205L Mutant Variant of Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:119.4 occ:0.88 OE2 A:GLU169 3.7 120.5 1.0 HD3 A:LYS168 4.5 96.0 1.0 CD A:GLU169 4.5 116.6 1.0 OE1 A:GLU169 4.6 117.7 1.0 HG2 A:LYS168 4.7 94.5 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of the Zn(II)-Bound Adcaii H205L 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 H205L Mutant Variant of Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn410 b:137.8 occ:0.95 OD2 A:ASP282 3.2 91.6 1.0 OD1 A:ASP282 3.3 77.4 1.0 H A:ASN285 3.5 76.8 1.0 CG A:ASP282 3.6 83.1 1.0 HA A:GLN284 3.7 85.9 1.0 O A:ASN285 3.7 90.0 1.0 HE1 A:TYR39 4.1 61.7 1.0 N A:ASN285 4.4 77.7 1.0 HG3 A:GLN284 4.5 92.1 1.0 O A:PRO283 4.6 30.0 1.0 CA A:GLN284 4.6 90.3 1.0 C A:ASN285 4.8 84.3 1.0 HH A:TYR39 4.8 65.4 1.0 CE1 A:TYR39 4.8 62.3 1.0 HE1 A:TYR42 4.8 79.9 1.0

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