Zinc in PDB 8qlg: Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1

The structure of Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1, PDB code: 8qlg was solved by M.Alcorlo, M.R.Abdullah, S.Hammerschmidt, J.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.27 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.038, 67.089, 109.448, 84.05, 87.26, 71.72
R / Rfree (%)	19.1 / 22.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 (pdb code 8qlg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 20 binding sites of Zinc where determined in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1, PDB code: 8qlg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1


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 Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:51.6 occ:1.00 OE2 A:GLU320 2.0 60.2 1.0 O A:GLY426 2.0 83.8 1.0 CD A:GLU320 2.7 54.2 1.0 OE1 A:GLU320 2.8 51.3 1.0 C A:GLY426 3.1 63.1 1.0 CA A:GLY426 3.7 58.7 1.0 N A:VAL427 4.1 49.2 1.0 CG A:GLU320 4.2 49.4 1.0 OG1 A:THR428 4.3 48.3 1.0 CA A:VAL427 4.5 49.9 1.0 OG A:SER324 4.8 40.7 1.0 O A:GLN425 4.9 62.2 1.0 N A:THR428 4.9 43.1 1.0 N A:GLY426 5.0 56.2 1.0

Zinc binding site 2 out of 20 in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1


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 Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:74.7 occ:1.00 O A:HOH827 2.3 51.1 1.0 OE1 A:GLU417 2.3 56.6 1.0 OE2 A:GLU417 2.6 56.3 1.0 CD A:GLU417 2.6 52.4 1.0 CG A:GLU417 3.8 51.6 1.0 OE1 A:GLU421 4.0 83.6 1.0 CB A:GLU417 4.1 47.1 1.0 CD A:LYS420 4.2 65.9 1.0 NZ A:LYS420 4.4 61.3 1.0 CA A:GLU417 4.8 45.3 1.0 CE A:LYS420 4.8 61.8 1.0 CG A:LYS420 5.0 65.5 1.0

Zinc binding site 3 out of 20 in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1


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 Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:43.5 occ:1.00 O A:HOH1068 2.1 51.6 1.0 O A:HOH992 2.1 45.9 1.0 O A:HOH1017 2.2 41.4 1.0 NE2 A:HIS244 2.2 38.1 1.0 O A:HOH1115 2.8 36.5 1.0 CD2 A:HIS244 3.1 29.1 1.0 CE1 A:HIS244 3.2 30.2 1.0 OE1 A:GLU243 3.7 37.6 1.0 ND1 A:HIS244 4.3 37.7 1.0 CG A:HIS244 4.3 37.2 1.0 CD A:GLU243 4.7 31.3 1.0 CB A:GLU243 4.8 25.8 1.0

Zinc binding site 4 out of 20 in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1


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 Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn704 b:42.7 occ:1.00 NE2 A:HIS233 2.2 36.4 1.0 O A:HOH1081 2.7 36.4 1.0 CD2 A:HIS233 3.1 29.6 1.0 CE1 A:HIS233 3.2 37.1 1.0 O A:HOH1111 4.1 45.2 1.0 ND1 A:HIS233 4.2 31.1 1.0 CG A:HIS233 4.2 31.8 1.0 CG A:PRO232 4.4 25.1 1.0 O A:HOH1074 4.4 54.5 1.0 CB A:PRO232 4.9 21.3 1.0

Zinc binding site 5 out of 20 in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1


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 Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn705 b:30.1 occ:1.00 NE2 A:HIS237 2.1 33.0 1.0 OD2 A:ASP238 2.3 37.5 1.0 OD1 A:ASP238 2.5 30.2 1.0 CG A:ASP238 2.7 31.0 1.0 CE1 A:HIS237 3.0 25.1 1.0 CD2 A:HIS237 3.1 30.6 1.0 O A:HOH1040 3.8 46.3 1.0 ND1 A:HIS237 4.1 28.1 1.0 CG A:HIS237 4.2 26.3 1.0 CB A:ASP238 4.2 21.7 1.0 O A:HOH996 4.7 29.8 1.0 CA A:ASP238 4.8 21.5 1.0 N A:ASP238 4.8 21.2 1.0 O A:HOH1015 4.9 45.9 1.0

Zinc binding site 6 out of 20 in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1


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 Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn706 b:59.0 occ:1.00 NE2 A:HIS71 2.0 53.3 1.0 O A:HOH970 2.1 54.4 1.0 O A:HOH915 2.5 49.3 1.0 CE1 A:HIS71 3.0 43.9 1.0 CD2 A:HIS71 3.0 43.7 1.0 OD1 A:ASN70 4.0 34.2 1.0 ND1 A:HIS71 4.1 44.6 1.0 CG A:HIS71 4.2 42.3 1.0 ND2 A:ASN70 4.3 35.1 1.0 CG A:ASN70 4.6 33.7 1.0

Zinc binding site 7 out of 20 in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1


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 Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn707 b:46.1 occ:1.00 NE2 A:HIS650 2.2 44.2 1.0 OE2 A:GLU646 2.3 48.5 1.0 O A:HOH1083 2.4 48.7 1.0 OE1 A:GLU646 2.4 44.1 1.0 O A:HOH1062 2.5 55.1 1.0 CD A:GLU646 2.6 47.5 1.0 CE1 A:HIS650 3.1 34.2 1.0 CD2 A:HIS650 3.2 39.0 1.0 O A:HOH1034 3.5 37.8 1.0 CG A:GLU646 4.1 49.5 1.0 ND1 A:HIS650 4.2 34.9 1.0 CG A:HIS650 4.3 38.7 1.0 O A:GLU646 4.6 39.8 1.0 O A:HOH1046 4.9 57.6 1.0

Zinc binding site 8 out of 20 in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1


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 Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn708 b:75.4 occ:1.00 O A:HOH843 2.1 38.5 1.0 NZ A:LYS332 2.3 53.5 1.0 OD1 A:ASP572 2.7 44.4 1.0 CE A:LYS332 3.5 34.2 1.0 CG A:ASP572 3.6 38.4 1.0 OD2 A:ASP572 3.8 38.0 1.0 O A:TYR389 3.9 66.9 1.0 O A:HOH1003 4.6 52.6 1.0 CB A:TYR389 4.6 65.2 1.0 CD A:LYS332 4.7 43.6 1.0 C A:TYR389 4.8 62.1 1.0 CB A:ASP572 5.0 35.7 1.0

Zinc binding site 9 out of 20 in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1


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 Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn709 b:102.1 occ:1.00 OD2 A:ASP516 2.4 60.1 1.0 O A:HOH1107 2.6 46.4 1.0 O A:HOH901 2.6 55.9 1.0 CG A:ASP516 3.2 50.1 1.0 ND2 A:ASN137 3.2 43.5 1.0 OD1 A:ASP516 3.2 54.5 1.0 OD1 A:ASP133 3.2 75.3 1.0 OE2 A:GLU515 3.9 75.7 1.0 O A:HOH849 4.3 39.9 1.0 CG A:ASP133 4.3 60.9 1.0 CG A:ASN137 4.5 49.6 1.0 CD A:GLU515 4.6 75.1 1.0 CB A:ASP516 4.6 39.3 1.0 OD2 A:ASP133 4.7 73.5 1.0 OE1 A:GLU515 4.8 74.2 1.0 O A:HOH1023 4.9 42.2 1.0 O A:HOH893 5.0 44.3 1.0

Zinc binding site 10 out of 20 in the Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1


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 Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn710 b:32.6 occ:1.00 OD2 A:ASP555 2.0 32.5 1.0 O A:HOH1077 2.5 34.4 1.0 OD1 A:ASP555 2.7 30.5 1.0 CG A:ASP555 2.7 36.9 1.0 CB A:ASP555 4.2 34.7 1.0 N A:LYS558 4.3 32.2 1.0 CB A:LYS558 4.3 30.5 1.0 O A:HOH969 4.5 38.5 1.0 CB A:ALA557 4.6 31.2 1.0 O A:HOH1051 4.7 34.7 1.0 CA A:LYS558 4.8 32.3 1.0 CE A:LYS558 4.9 54.3 1.0

M.Alcorlo, M.R.Abdullah, S.Hammerschmidt, J.Hermoso. Crystal Structure of the Pneumococcal Substrate-Binding Protein Alid in Closed Conformation in Complex with Peptide 1 To Be Published.