Zinc in PDB 5c0q: Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana

All present enzymatic activity of Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana:
3.2.1.52;

The structure of Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana, PDB code: 5c0q was solved by N.C.Ha, J.S.Kim, B.Y.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	158.843, 158.843, 520.569, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 24.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana (pdb code 5c0q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 35 binding sites of Zinc where determined in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana, PDB code: 5c0q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 35 in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana


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 Zn Bound Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:52.6 occ:1.00 ND1 A:HIS161 1.9 25.9 1.0 OD2 A:ASP117 2.1 24.3 1.0 NE2 A:HIS165 2.3 26.7 1.0 CE1 A:HIS161 2.4 29.2 1.0 CE1 A:HIS165 3.0 23.3 1.0 CG A:ASP117 3.1 24.3 1.0 CG A:HIS161 3.2 26.8 1.0 CD2 A:HIS165 3.3 27.1 1.0 OD1 A:ASP117 3.6 24.5 1.0 NE2 A:HIS161 3.7 30.1 1.0 N A:HIS161 3.8 24.0 1.0 CB A:HIS161 4.0 22.0 1.0 ND1 A:HIS165 4.1 26.8 1.0 CD2 A:HIS161 4.1 26.8 1.0 CB A:ASP117 4.2 17.3 1.0 CG A:HIS165 4.2 28.8 1.0 C A:LYS160 4.5 19.0 1.0 CA A:HIS161 4.5 23.4 1.0 CG1 A:VAL115 4.5 15.7 1.0 O A:LYS160 4.8 19.0 1.0

Zinc binding site 2 out of 35 in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana


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 Zn Bound Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:78.7 occ:1.00 ND1 A:HIS173 2.0 40.5 1.0 OD1 A:ASP171 2.3 48.9 1.0 OD2 A:ASP171 2.3 45.0 1.0 CG A:ASP171 2.7 45.5 1.0 CE1 A:HIS173 2.8 40.6 1.0 CG A:HIS173 3.1 45.3 1.0 CB A:HIS173 3.6 42.6 1.0 NE2 A:HIS173 4.0 40.3 1.0 CD2 A:HIS173 4.1 41.3 1.0 CB A:ASP171 4.2 40.5 1.0 N A:HIS173 4.3 40.1 1.0 CA A:HIS173 4.6 41.9 1.0 N A:SER172 4.8 32.4 1.0 CA A:ASP171 5.0 38.0 1.0

Zinc binding site 3 out of 35 in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana


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 Zn Bound Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:70.9 occ:1.00 OE2 A:GLU189 2.5 54.1 1.0 OE1 A:GLU189 2.7 44.0 1.0 CD A:GLU189 2.9 44.6 1.0 OE2 A:GLU185 3.1 39.8 1.0 CD A:GLU185 3.8 41.4 1.0 CG A:GLU185 4.0 34.4 1.0 NH2 A:ARG188 4.2 44.8 1.0 CE A:LYS167 4.4 30.8 1.0 CG A:GLU189 4.5 31.2 1.0 NZ A:LYS167 4.5 27.4 1.0 OE1 A:GLU185 4.9 54.6 1.0

Zinc binding site 4 out of 35 in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana


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 Zn Bound Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:60.9 occ:1.00 OE2 A:GLU327 1.8 35.7 1.0 OE2 A:GLU330 2.4 46.5 1.0 NH1 A:ARG54 2.6 53.1 1.0 CD A:GLU327 2.7 32.9 1.0 NH2 A:ARG54 2.8 52.9 1.0 OE1 A:GLU327 3.0 28.5 1.0 CZ A:ARG54 3.1 50.2 1.0 CD A:GLU330 3.1 44.2 1.0 OE1 A:GLU330 3.2 45.5 1.0 CG A:GLU327 4.1 26.7 1.0 NE A:ARG54 4.3 44.0 1.0 CG A:GLU330 4.6 32.5 1.0 ND2 A:ASN50 4.9 29.9 1.0 NH1 A:ARG331 5.0 15.7 1.0

Zinc binding site 5 out of 35 in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana


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 Zn Bound Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:21.9 occ:1.00 OE2 A:GLU346 1.2 13.3 1.0 OE2 A:GLU398 1.8 24.6 1.0 CD A:GLU346 2.4 24.5 1.0 CD A:GLU398 2.6 24.4 1.0 OE1 A:GLU398 2.7 32.8 1.0 CG A:GLU346 3.1 22.3 1.0 OE1 A:GLU346 3.4 24.5 1.0 CG A:GLU398 4.1 18.9 1.0 NH2 A:ARG381 4.1 23.1 1.0 CB A:GLU346 4.4 19.0 1.0 N A:GLU346 4.6 20.3 1.0

Zinc binding site 6 out of 35 in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana


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 Zn Bound Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:49.1 occ:1.00 NZ B:LYS86 1.9 31.3 1.0 NE2 A:HIS448 2.3 22.4 1.0 OE2 A:GLU334 2.6 39.0 1.0 CE B:LYS86 2.6 38.1 1.0 CD2 A:HIS448 3.2 18.3 1.0 CE1 A:HIS448 3.4 21.9 1.0 CD A:GLU334 3.8 38.8 1.0 CD B:LYS86 4.0 21.2 1.0 CB A:PRO433 4.2 32.5 1.0 OE1 A:GLU334 4.4 51.4 1.0 CG A:HIS448 4.4 20.1 1.0 CG2 A:ILE446 4.4 19.5 1.0 ND1 A:HIS448 4.4 20.9 1.0 CG B:LYS86 4.6 18.6 1.0 CG A:PRO433 4.7 35.8 1.0 CD1 A:ILE446 5.0 19.1 1.0 CG A:GLU334 5.0 24.9 1.0

Zinc binding site 7 out of 35 in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana


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 Zn Bound Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:71.2 occ:1.00 CE1 A:HIS461 2.2 45.9 1.0 ND1 A:HIS461 3.1 42.5 1.0 NE2 A:HIS461 3.1 45.2 1.0 O A:ILE333 3.8 29.6 1.0 CG A:HIS461 4.2 39.5 1.0 CD2 A:HIS461 4.2 48.3 1.0 O A:GLU330 4.3 21.6 1.0 CD A:ARG465 4.5 61.5 1.0 NH1 A:ARG465 4.6 52.3 1.0 NE A:ARG465 4.9 61.0 1.0 C A:ILE333 4.9 24.5 1.0 CZ A:ARG465 4.9 60.2 1.0

Zinc binding site 8 out of 35 in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana


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 Zn Bound Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1008 b:90.2 occ:1.00 OD2 A:ASP245 2.8 29.6 1.0 NE2 A:HIS161 3.0 30.1 1.0 CE1 A:HIS161 3.5 29.2 1.0 CG A:ASP245 3.7 25.6 1.0 OD1 A:ASP245 3.8 29.4 1.0 CD2 A:HIS161 3.9 26.8 1.0 CE1 A:HIS173 4.4 40.6 1.0 ND1 A:HIS161 4.5 25.9 1.0 CG A:HIS161 4.7 26.8 1.0 SD A:MET249 4.8 39.9 1.0

Zinc binding site 9 out of 35 in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana


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 Zn Bound Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1009 b:0.1 occ:1.00 OE2 A:GLU303 2.8 70.2 1.0 CD A:GLU303 3.6 66.9 1.0 OE1 A:GLU303 3.7 67.2 1.0 CD A:ARG299 3.9 57.8 1.0 CG A:ARG299 4.6 45.9 1.0 NE A:ARG299 5.0 61.6 1.0

Zinc binding site 10 out of 35 in the Crystal Structure of Zn Bound Cbsa From Thermotoga Neapolitana


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 Zn Bound Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1010 b:48.3 occ:1.00 NE2 B:HIS448 2.3 23.0 1.0 OE1 B:GLU334 2.4 38.8 1.0 NZ A:LYS86 2.5 37.9 1.0 CD2 B:HIS448 3.3 18.6 1.0 CE1 B:HIS448 3.3 23.6 1.0 CD B:GLU334 3.4 41.1 1.0 CE A:LYS86 3.6 27.0 1.0 OE2 B:GLU334 3.8 45.5 1.0 CD A:LYS86 3.9 22.4 1.0 CB B:PRO433 4.4 32.2 1.0 ND1 B:HIS448 4.4 21.6 1.0 CG B:HIS448 4.5 18.6 1.0 CG2 B:ILE446 4.6 22.2 1.0 CG B:GLU334 4.6 26.4 1.0 CG B:PRO433 4.9 32.3 1.0 CG A:LYS86 4.9 19.3 1.0 CD1 B:ILE446 5.0 26.4 1.0

J.S.Kim, B.Y.Yoon, J.Ahn, J.Cha, N.C.Ha. Crystal Structure of Beta-N-Acetylglucosaminidase Cbsa From Thermotoga Neapolitana Biochem.Biophys.Res.Commun. V. 464 869 2015.
ISSN: ESSN 1090-2104
PubMed: 26187666
DOI: 10.1016/J.BBRC.2015.07.053