Zinc in PDB 5w6p: Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211)

The structure of Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211), PDB code: 5w6p was solved by M.Plattner, M.M.Shneider, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.68 / 2.34
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.519, 303.227, 113.207, 90.00, 90.38, 90.00
R / Rfree (%)	15.4 / 19

The structure of Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) also contains other interesting chemical elements:

Potassium

(K)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) (pdb code 5w6p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 40 binding sites of Zinc where determined in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211), PDB code: 5w6p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 40 in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211)


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 Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:58.4 occ:1.00 O A:HOH1384 2.2 50.1 1.0 O A:HOH1439 2.4 45.3 1.0 OD1 A:ASP366 2.5 39.8 1.0 O A:HOH1393 2.5 45.4 1.0 CG A:ASP366 3.2 39.9 1.0 OD2 A:ASP366 3.3 44.5 1.0 O A:HOH1412 4.0 46.3 1.0 O A:HOH1167 4.2 44.4 1.0 N A:GLY344 4.3 42.6 1.0 O A:ALA367 4.3 37.3 1.0 N A:ALA367 4.3 30.7 1.0 CB A:ALA367 4.6 31.8 1.0 CB A:ASP366 4.7 32.9 1.0 CA A:ALA367 4.9 33.2 1.0 CA A:GLY344 4.9 35.3 1.0

Zinc binding site 2 out of 40 in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211)


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 Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:84.6 occ:1.00 O A:GLY872 4.4 49.0 1.0 O A:HOH1410 4.5 16.9 1.0

Zinc binding site 3 out of 40 in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211)


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 Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:37.1 occ:1.00 OD2 A:ASP868 1.9 62.5 1.0 O A:HOH1377 2.1 22.6 1.0 NE2 A:HIS774 2.2 39.3 1.0 O A:HOH1410 2.3 16.9 1.0 CG A:ASP868 3.0 51.3 1.0 CD2 A:HIS774 3.1 37.4 1.0 CE1 A:HIS774 3.2 38.1 1.0 CB A:ASP868 3.6 41.1 1.0 N A:GLY765 3.9 44.0 1.0 OD1 A:ASP868 4.0 57.4 1.0 CG A:HIS774 4.2 37.1 1.0 ND1 A:HIS774 4.2 38.3 1.0 CA A:GLY765 4.5 38.8 1.0 O A:GLY765 4.5 37.7 1.0 CA A:GLY873 4.7 45.9 1.0 C A:GLY765 4.7 41.2 1.0 CA A:SER764 4.8 41.5 1.0 C A:SER764 4.8 41.1 1.0 CA A:ASP868 4.9 43.5 1.0

Zinc binding site 4 out of 40 in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211)


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 Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:66.0 occ:1.00 OG A:SER443 2.2 51.9 1.0 O A:HOH1128 2.4 44.1 1.0 O A:HOH1210 2.4 45.5 1.0 OD2 A:ASP407 2.5 41.9 1.0 O A:HOH1447 2.5 51.9 1.0 CB A:SER443 3.1 44.4 1.0 CG A:ASP407 3.3 37.9 1.0 OD1 A:ASP407 3.5 35.8 1.0 N A:SER443 3.9 42.2 1.0 OE2 A:GLU440 4.0 43.5 1.0 CA A:SER443 4.1 47.4 1.0 CB A:ALA455 4.6 41.9 1.0 CB A:ASP407 4.7 36.0 1.0 O A:THR441 4.7 38.3 1.0 CD A:GLU440 4.7 42.1 1.0 C A:PRO442 4.9 37.1 1.0

Zinc binding site 5 out of 40 in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211)


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 Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:32.1 occ:1.00 OD2 C:ASP488 2.1 54.9 1.0 OD2 B:ASP488 2.2 41.8 1.0 OD2 A:ASP488 2.3 39.7 1.0 O B:HOH1391 2.3 14.1 1.0 CG B:ASP488 3.0 36.1 1.0 CG C:ASP488 3.0 40.8 1.0 CG A:ASP488 3.0 39.7 1.0 OD1 B:ASP488 3.1 37.8 1.0 OD1 A:ASP488 3.1 36.3 1.0 OD1 C:ASP488 3.2 43.0 1.0 O C:HOH1225 4.0 44.7 1.0 O A:HOH1327 4.2 49.4 1.0 CB C:ASP488 4.4 32.4 1.0 CB B:ASP488 4.4 32.9 1.0 CB A:ASP488 4.4 24.3 1.0 OG1 A:THR510 4.5 36.6 1.0 OG1 C:THR510 4.6 35.9 1.0 OG1 B:THR510 4.6 40.3 1.0

Zinc binding site 6 out of 40 in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211)


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 Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:57.2 occ:1.00 OD1 A:ASP699 2.4 39.6 1.0 OD2 A:ASP699 2.6 41.3 1.0 CG A:ASP699 2.9 43.4 1.0 O A:HOH1430 3.7 44.8 1.0 O A:HOH1395 3.9 44.3 1.0 CB A:ASP699 4.4 38.2 1.0 O A:GLY700 4.5 49.1 1.0 O A:HOH1301 4.7 41.2 1.0 N A:GLY700 4.8 39.4 1.0

Zinc binding site 7 out of 40 in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211)


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 Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:89.6 occ:1.00 OD2 A:ASP272 2.1 0.3 1.0 O B:HOH1383 2.7 51.7 1.0 ND1 A:HIS268 2.7 69.2 1.0 CG A:ASP272 3.0 86.4 1.0 OD1 A:ASP272 3.3 93.2 1.0 CB A:HIS268 3.3 55.9 1.0 CG A:HIS268 3.4 66.5 1.0 CE1 A:HIS268 3.9 70.2 1.0 N A:HIS268 4.2 46.3 1.0 CA A:HIS268 4.3 51.5 1.0 CB A:ASP272 4.3 66.1 1.0 ND2 B:ASN258 4.6 61.0 1.0 CD2 A:HIS268 4.6 69.3 1.0 C A:HIS268 4.8 53.8 1.0 NE2 A:HIS268 4.8 70.5 1.0

Zinc binding site 8 out of 40 in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211)


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 Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:45.2 occ:0.50 O B:HOH1141 1.8 49.1 0.5 OE1 B:GLU473 2.1 61.9 1.0 O B:HOH1283 2.4 55.6 1.0 CD B:GLU473 3.1 53.1 1.0 OE2 B:GLU473 3.4 54.6 1.0 CG B:GLU473 4.4 46.6 1.0 O B:HOH1156 5.0 42.1 1.0

Zinc binding site 9 out of 40 in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211)


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 Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:58.0 occ:1.00 O B:HOH1365 2.1 52.4 1.0 O B:HOH1116 2.2 52.9 1.0 O B:HOH1379 2.5 44.2 1.0 OD1 B:ASP366 2.5 42.5 1.0 O B:HOH1247 2.7 46.2 1.0 CG B:ASP366 3.2 43.2 1.0 OD2 B:ASP366 3.2 45.0 1.0 O B:HOH1304 4.1 37.6 1.0 O B:HOH1390 4.3 42.1 1.0 O B:ALA367 4.3 41.0 1.0 N B:GLY344 4.3 44.9 1.0 N B:ALA367 4.3 33.6 1.0 O B:HOH1130 4.4 48.6 1.0 CB B:ASP366 4.6 42.0 1.0 CB B:ALA367 4.6 36.5 1.0 CA B:ALA367 4.9 35.6 1.0 CA B:GLY344 4.9 45.4 1.0

Zinc binding site 10 out of 40 in the Crystal Structure of Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211)


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 Bacteriophage CBA120 Tailspike Protein 2 Enzymatically Active Domain (TSP2DN, ORF211) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:0.4 occ:1.00 OD2 B:ASP768 2.6 70.5 1.0 O B:HOH1373 3.0 63.3 1.0 CG B:ASP768 3.3 64.6 1.0 OD1 B:ASP768 3.4 59.6 1.0 O B:GLY795 4.2 66.6 1.0 OG1 B:THR796 4.6 56.5 1.0 CA B:THR796 4.7 54.8 1.0 CB B:ASP768 4.8 62.4 1.0

M.Plattner, M.M.Shneider, N.P.Arbatsky, A.S.Shashkov, A.O.Chizhov, S.Nazarov, N.S.Prokhorov, N.M.I.Taylor, S.A.Buth, M.Gambino, Y.E.Gencay, L.Brondsted, E.M.Kutter, Y.A.Knirel, P.G.Leiman. Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120. J.Mol.Biol. V. 431 3718 2019.
ISSN: ESSN 1089-8638
PubMed: 31325442
DOI: 10.1016/J.JMB.2019.07.022