Zinc in PDB 3rcc: Crystal Structure of the Streptococcus Agalactiae Sortase A

The structure of Crystal Structure of the Streptococcus Agalactiae Sortase A, PDB code: 3rcc was solved by B.Khare, S.V.L.Narayana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.23 / 3.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	237.674, 167.759, 97.536, 90.00, 93.55, 90.00
R / Rfree (%)	23.2 / 29.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 73;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Streptococcus Agalactiae Sortase A (pdb code 3rcc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 73 binding sites of Zinc where determined in the Crystal Structure of the Streptococcus Agalactiae Sortase A, PDB code: 3rcc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 73 in the Crystal Structure of the Streptococcus Agalactiae Sortase A


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 Streptococcus Agalactiae Sortase A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:48.8 occ:1.00 OE2 A:GLU93 2.0 58.7 1.0 NE2 A:HIS66 2.2 82.0 1.0 OE1 B:GLU80 2.4 46.6 1.0 OE2 B:GLU80 2.6 42.5 1.0 CD B:GLU80 2.8 46.3 1.0 CE1 A:HIS66 2.8 82.7 1.0 CD A:GLU93 2.9 58.5 1.0 OE1 A:GLU93 3.3 58.9 1.0 CD2 A:HIS66 3.4 82.6 1.0 O A:ASN67 3.7 79.6 1.0 ND1 A:HIS66 4.0 83.1 1.0 CG A:GLU93 4.2 56.1 1.0 CG B:GLU80 4.3 47.1 1.0 CG A:HIS66 4.3 82.8 1.0 C A:ASN67 4.9 79.5 1.0

Zinc binding site 2 out of 73 in the Crystal Structure of the Streptococcus Agalactiae Sortase A


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 Streptococcus Agalactiae Sortase A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:49.9 occ:1.00 NE2 A:HIS118 1.6 34.9 1.0 O B:HOH401 2.0 46.8 1.0 O B:HOH402 2.2 28.7 1.0 NE2 B:HIS136 2.3 51.1 1.0 CE1 A:HIS118 2.5 35.9 1.0 CD2 A:HIS118 2.7 37.0 1.0 CD2 B:HIS136 3.2 51.4 1.0 CE1 B:HIS136 3.2 51.5 1.0 ND1 A:HIS118 3.7 36.9 1.0 CG A:HIS118 3.8 38.1 1.0 ND1 B:HIS136 4.4 51.1 1.0 CG B:HIS136 4.4 50.9 1.0 CD1 A:LEU94 4.4 50.5 1.0 CB A:CYS184 4.9 62.2 1.0 CE1 B:PHE131 5.0 56.5 1.0

Zinc binding site 3 out of 73 in the Crystal Structure of the Streptococcus Agalactiae Sortase A


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 Streptococcus Agalactiae Sortase A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:58.0 occ:1.00 OE1 A:GLU168 1.9 58.6 1.0 NE2 A:HIS196 2.0 64.7 1.0 CE1 A:HIS196 2.1 65.0 1.0 OE1 L:GLU158 2.2 43.3 1.0 O L:HOH401 2.3 59.8 1.0 CD A:GLU168 2.6 57.6 1.0 OE2 A:GLU168 2.7 57.3 1.0 OE2 L:GLU158 2.9 44.4 1.0 CD L:GLU158 2.9 44.7 1.0 CD2 A:HIS196 3.3 65.0 1.0 ND1 A:HIS196 3.4 65.1 1.0 O A:HOH401 3.6 18.0 1.0 OG L:SER160 3.8 43.9 1.0 CG A:HIS196 4.0 64.8 1.0 CG A:GLU168 4.1 55.6 1.0 NE2 A:HIS166 4.2 49.0 1.0 CG2 A:ILE194 4.2 58.1 1.0 CG L:GLU158 4.3 45.1 1.0 CE1 A:HIS166 4.5 50.0 1.0 CD1 A:ILE194 4.7 56.9 1.0 CB A:ILE194 4.7 58.2 1.0 CB A:GLU168 4.9 54.0 1.0

Zinc binding site 4 out of 73 in the Crystal Structure of the Streptococcus Agalactiae Sortase A


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 Streptococcus Agalactiae Sortase A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:76.3 occ:1.00 OE2 A:GLU135 2.2 61.6 1.0 OE2 L:GLU165 2.3 59.8 1.0 OE2 A:GLU191 2.8 69.3 1.0 CD A:GLU135 3.0 60.5 1.0 CD L:GLU165 3.3 58.9 1.0 OE1 A:GLU135 3.3 61.2 1.0 CD A:GLU191 3.5 70.8 1.0 OE1 A:GLU191 3.5 71.0 1.0 OE1 L:GLU165 3.6 59.6 1.0 CG A:GLU135 4.2 57.0 1.0 NZ A:LYS161 4.3 52.7 1.0 CD A:LYS161 4.6 51.7 1.0 CG L:GLU165 4.7 55.1 1.0 CG A:GLU191 4.9 70.1 1.0

Zinc binding site 5 out of 73 in the Crystal Structure of the Streptococcus Agalactiae Sortase A


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 Streptococcus Agalactiae Sortase A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:95.9 occ:1.00 OE2 L:GLU135 2.4 60.5 1.0 OE2 A:GLU165 2.8 66.3 1.0 CD L:GLU135 3.2 59.4 1.0 OE1 L:GLU135 3.2 60.3 1.0 OE1 A:GLU165 3.4 65.0 1.0 CD A:GLU165 3.4 63.9 1.0 NZ L:LYS161 4.1 46.8 1.0 CD L:LYS161 4.4 46.4 1.0 CG L:GLU135 4.7 57.1 1.0 CE L:LYS161 4.7 47.0 1.0 CD1 L:ILE193 4.8 49.6 1.0 CG A:GLU165 4.9 57.2 1.0

Zinc binding site 6 out of 73 in the Crystal Structure of the Streptococcus Agalactiae Sortase A


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 Streptococcus Agalactiae Sortase A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:68.3 occ:1.00 OE1 C:GLU80 1.8 50.5 1.0 NE2 B:HIS66 2.1 83.2 1.0 OE2 B:GLU93 2.3 56.0 1.0 CE1 B:HIS66 2.7 84.1 1.0 OE1 B:GLU93 2.7 57.3 1.0 CD C:GLU80 2.8 49.1 1.0 CD B:GLU93 2.8 55.1 1.0 CD2 B:HIS66 3.0 83.3 1.0 OE2 C:GLU80 3.1 48.0 1.0 O B:ASN67 3.6 78.3 1.0 ND1 B:HIS66 3.7 84.1 1.0 CG B:HIS66 3.8 83.1 1.0 CG C:GLU80 4.2 47.8 1.0 CG B:GLU93 4.3 52.7 1.0 C B:ASN67 4.4 78.2 1.0 OG1 B:THR92 4.5 53.6 1.0 CD B:PRO69 4.6 71.5 1.0 CB C:GLU80 4.6 46.8 1.0 N B:ASN67 4.7 80.4 1.0

Zinc binding site 7 out of 73 in the Crystal Structure of the Streptococcus Agalactiae Sortase A


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 Streptococcus Agalactiae Sortase A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:36.2 occ:1.00 NE2 B:HIS118 1.9 30.2 1.0 NE2 C:HIS136 2.0 42.5 1.0 O B:HOH403 2.1 2.0 1.0 O B:HOH404 2.7 8.0 1.0 CE1 B:HIS118 2.8 30.1 1.0 CE1 C:HIS136 2.9 43.4 1.0 CD2 B:HIS118 3.0 32.3 1.0 CD2 C:HIS136 3.0 43.8 1.0 ND1 B:HIS118 4.0 31.2 1.0 ND1 C:HIS136 4.0 43.8 1.0 CG B:HIS118 4.1 35.4 1.0 CG C:HIS136 4.1 44.4 1.0 CB B:CYS184 4.4 58.1 1.0 CD1 B:LEU94 4.7 46.0 1.0 CG C:GLU135 4.8 50.6 1.0

Zinc binding site 8 out of 73 in the Crystal Structure of the Streptococcus Agalactiae Sortase A


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 Streptococcus Agalactiae Sortase A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:55.9 occ:1.00 OE1 K:GLU158 2.0 40.7 1.0 OE1 B:GLU168 2.1 54.8 1.0 CE1 B:HIS196 2.1 55.3 1.0 O K:HOH401 2.3 22.0 1.0 NE2 B:HIS196 2.3 55.0 1.0 OE2 B:GLU168 2.6 54.1 1.0 CD K:GLU158 2.6 40.7 1.0 CD B:GLU168 2.6 53.7 1.0 OE2 K:GLU158 2.7 40.5 1.0 ND1 B:HIS196 3.4 55.3 1.0 CD2 B:HIS196 3.7 54.7 1.0 NE2 B:HIS166 3.9 44.1 1.0 CE1 B:HIS166 4.0 45.5 1.0 CG K:GLU158 4.0 40.2 1.0 CG2 B:ILE194 4.1 48.7 1.0 CG B:GLU168 4.2 51.2 1.0 CG B:HIS196 4.2 53.9 1.0 CB B:ILE194 4.6 48.5 1.0 OG K:SER160 4.6 43.7 1.0 CB B:GLU168 4.9 49.8 1.0 CG1 B:ILE194 4.9 49.3 1.0

Zinc binding site 9 out of 73 in the Crystal Structure of the Streptococcus Agalactiae Sortase A


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 Streptococcus Agalactiae Sortase A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:97.5 occ:1.00 OE2 B:GLU135 3.3 57.7 1.0 OE1 K:GLU165 3.6 61.2 1.0 OE2 K:GLU165 3.7 58.6 1.0 CD K:GLU165 3.7 58.5 1.0 CD B:GLU135 4.0 57.8 1.0 OE1 B:GLU135 4.3 57.4 1.0 NZ B:LYS161 4.3 48.5 1.0 CB K:GLU165 4.6 49.6 1.0 CG K:GLU165 4.7 53.5 1.0 CD B:LYS161 4.8 45.7 1.0 OG1 A:THR190 4.9 72.0 1.0

Zinc binding site 10 out of 73 in the Crystal Structure of the Streptococcus Agalactiae Sortase A


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 Streptococcus Agalactiae Sortase A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:47.2 occ:1.00 NE2 B:HIS119 2.1 38.9 1.0 CD2 B:HIS119 3.1 37.5 1.0 CE1 B:HIS119 3.1 37.3 1.0 O B:PHE121 3.7 51.1 1.0 C B:PHE121 3.9 49.7 1.0 CD2 B:LEU83 4.0 47.2 1.0 ND1 B:HIS119 4.2 37.6 1.0 CG B:HIS119 4.2 38.5 1.0 O B:VAL120 4.7 44.9 1.0

B.Khare, V.Krishnan, K.R.Rajashankar, H.I-Hsiu, M.Xin, H.Ton-That, S.V.Narayana. Structural Differences Between the Streptococcus Agalactiae Housekeeping and Pilus-Specific Sortases: Srta and SRTC1. Plos One V. 6 22995 2011.
ISSN: ESSN 1932-6203
PubMed: 21912586
DOI: 10.1371/JOURNAL.PONE.0022995