Zinc in PDB 4kjm: Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb

The structure of Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb, PDB code: 4kjm was solved by M.Cymborowski, I.G.Shabalin, G.Joachimiak, M.Chruszcz, P.Gornicki, R.Zhang, A.Joachimiak, W.Minor, Midwest Center For Structural Genomics, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.28 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.783, 59.230, 88.186, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23

The structure of Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	2 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb (pdb code 4kjm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb, PDB code: 4kjm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb


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 Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:27.2 occ:0.50 O A:HOH430 1.8 23.9 0.4 OD1 A:ASP13 1.9 31.9 1.0 O A:HOH428 2.0 24.4 0.5 O B:HOH437 2.0 26.1 0.5 O B:HOH394 2.4 17.4 0.5 CL B:CL210 2.4 27.6 1.0 ZN A:ZN204 2.6 32.2 0.4 CG A:ASP13 2.8 36.4 1.0 OD2 A:ASP13 3.2 31.8 1.0 O A:HOH330 3.7 38.2 1.0 CB A:ASP13 4.1 41.0 1.0 CB B:SER20 4.2 20.2 1.0 O A:ASP13 4.3 28.0 1.0 N B:GLN21 4.3 22.4 1.0 O A:HOH303 4.4 31.3 1.0 O A:HOH429 4.4 33.6 0.4 CA B:SER20 4.4 21.0 1.0 CA A:ASP13 4.6 35.8 1.0 CA A:GLY16 4.7 23.6 1.0 O B:HOH361 4.8 40.3 1.0 C A:ASP13 4.9 30.7 1.0 CB B:GLN21 4.9 23.0 1.0 C B:SER20 4.9 22.3 1.0 O A:HOH407 4.9 34.7 0.6 C A:GLY16 5.0 22.9 1.0 N A:THR17 5.0 22.6 1.0

Zinc binding site 2 out of 18 in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb


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 Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:32.2 occ:0.40 CL B:CL210 2.0 27.6 1.0 O A:HOH430 2.0 23.9 0.4 O A:HOH429 2.0 33.6 0.4 O A:HOH407 2.3 34.7 0.6 ZN A:ZN203 2.6 27.2 0.5 OD2 A:ASP13 2.7 31.8 1.0 O A:HOH428 3.3 24.4 0.5 CG A:ASP13 3.4 36.4 1.0 OD1 A:ASP13 3.4 31.9 1.0 NZ A:LYS69 3.5 54.3 1.0 CB B:ASN22 4.4 24.0 1.0 O B:HOH437 4.4 26.1 0.5 CB B:SER20 4.5 20.2 1.0 CE A:LYS69 4.6 43.9 1.0 CB A:ASP13 4.7 41.0 1.0 O A:HOH307 4.7 35.7 1.0 O B:HOH394 4.8 17.4 0.5 O B:HOH322 4.8 43.9 1.0 OG1 A:THR17 4.9 26.5 1.0 N B:ASN22 4.9 22.2 1.0

Zinc binding site 3 out of 18 in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb


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 Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:55.0 occ:0.50 O A:HOH431 2.0 44.9 0.5 O A:HOH433 2.0 52.8 0.5 O A:HOH432 2.0 32.9 0.5 OD1 A:ASP118 2.3 33.3 1.0 OD2 A:ASP118 2.7 33.8 1.0 CG A:ASP118 2.9 31.3 1.0 O A:HOH396 3.8 32.1 0.5 O A:HOH405 4.0 35.4 0.5 O A:SER114 4.3 26.7 1.0 CB A:ASP118 4.4 26.9 1.0 CB A:SER114 4.6 28.2 1.0 C A:SER114 5.0 25.9 1.0

Zinc binding site 4 out of 18 in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb


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 Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:52.0 occ:0.70 O A:HOH435 2.0 46.4 0.7 O A:HOH434 2.0 37.8 0.7 O A:HOH412 2.1 23.8 0.3 NE2 A:HIS121 2.3 49.3 1.0 O A:HOH406 2.6 20.2 0.3 OE1 A:GLU125 2.7 58.4 1.0 CE1 A:HIS121 3.1 50.6 1.0 CD2 A:HIS121 3.5 46.1 1.0 CD A:GLU125 3.5 50.9 1.0 O A:HOH444 3.8 54.5 0.4 CG A:GLU125 4.0 50.9 1.0 O A:HOH317 4.1 36.1 1.0 ND1 A:HIS121 4.3 47.3 1.0 CB A:GLU125 4.4 44.7 1.0 OE2 A:GLU125 4.5 56.1 1.0 CG A:HIS121 4.5 45.4 1.0 ZN A:ZN209 4.7 64.7 0.4

Zinc binding site 5 out of 18 in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb


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 Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:56.9 occ:0.50 O A:HOH411 1.8 27.8 0.5 O A:HOH438 2.0 53.0 0.5 O A:HOH437 2.0 44.5 0.5 O A:HOH436 2.0 48.8 0.5 ND1 A:HIS121 2.3 47.3 1.0 CG A:HIS121 3.2 45.4 1.0 CE1 A:HIS121 3.2 50.6 1.0 CB A:HIS121 3.4 40.5 1.0 CA A:HIS121 3.7 38.2 1.0 NE2 A:HIS121 4.3 49.3 1.0 CD2 A:HIS121 4.3 46.1 1.0 O A:HIS121 4.6 33.5 1.0 C A:HIS121 4.6 35.7 1.0 N A:HIS121 4.7 35.4 1.0

Zinc binding site 6 out of 18 in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb


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 Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn208 b:57.5 occ:0.40 O A:HOH441 2.0 41.8 0.4 O A:HOH439 2.0 50.6 0.4 O A:HOH440 2.0 34.6 0.4 ND1 A:HIS70 2.3 56.2 1.0 CE1 A:HIS70 3.2 61.6 1.0 CG A:HIS70 3.3 48.9 1.0 O A:HOH401 3.4 37.4 0.6 CB A:HIS70 3.5 39.2 1.0 CA A:HIS70 4.0 33.5 1.0 O A:HOH343 4.1 38.5 0.6 O B:HOH440 4.3 64.0 0.4 NE2 A:HIS70 4.3 61.2 1.0 CD2 A:HIS70 4.4 57.4 1.0 N A:HIS70 4.7 28.5 1.0

Zinc binding site 7 out of 18 in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb


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 Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn209 b:64.7 occ:0.40 O A:HOH444 2.0 54.5 0.4 O A:HOH442 2.0 55.3 0.4 O A:HOH443 2.0 50.0 0.4 OE2 A:GLU125 2.6 56.1 1.0 OE1 A:GLU125 3.0 58.4 1.0 CD A:GLU125 3.1 50.9 1.0 O A:HOH418 4.0 62.0 1.0 O A:HOH412 4.2 23.8 0.3 CG A:GLU125 4.6 50.9 1.0 ZN A:ZN206 4.7 52.0 0.7 O A:HOH435 4.9 46.4 0.7

Zinc binding site 8 out of 18 in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb


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 Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn210 b:57.0 occ:0.40 O A:HOH446 2.0 50.8 0.4 O A:HOH445 2.0 56.0 0.4 O B:HOH442 2.0 57.6 0.4 O B:HOH441 2.0 55.5 0.4 O B:HOH413 2.2 40.0 0.6 O A:HOH415 2.4 54.3 0.6 O A:HOH416 3.2 34.8 0.6 ND2 B:ASN108 3.7 39.6 1.0 O B:HOH400 4.3 47.9 1.0 CB A:MSE4 4.3 46.8 1.0 CG A:MSE4 4.6 56.7 1.0 CG B:ASN108 4.7 36.2 1.0 CB B:ASN108 4.7 34.0 1.0 N A:THR1 4.9 76.7 1.0

Zinc binding site 9 out of 18 in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb


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 Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn211 b:81.9 occ:1.00 O A:HOH447 2.0 68.5 1.0 O A:HOH448 2.0 64.7 1.0 OD2 A:ASP94 2.2 72.2 1.0 OD1 A:ASP94 2.5 74.2 1.0 CG A:ASP94 2.7 65.2 1.0 CB A:ASP94 4.3 60.1 1.0 O A:HOH409 4.6 65.7 1.0 OG A:SER93 4.6 63.6 1.0

Zinc binding site 10 out of 18 in the Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb


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 Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:50.3 occ:0.60 O B:HOH421 2.0 36.9 0.6 O B:HOH423 2.0 39.6 0.6 O B:HOH422 2.0 47.5 0.6 OD2 B:ASP27 2.4 47.3 1.0 O B:HOH414 2.6 30.8 0.4 OD1 B:ASP27 3.0 39.7 1.0 CG B:ASP27 3.0 40.6 1.0 O B:HOH369 3.6 48.8 1.0 ND2 B:ASN73 4.3 33.3 1.0 CB B:ASP27 4.4 39.1 1.0 OD1 B:ASN77 4.7 27.7 1.0 NZ B:LYS30 4.8 46.0 1.0

M.Cymborowski, I.G.Shabalin, G.Joachimiak, M.Chruszcz, P.Gornicki, R.Zhang, A.Joachimiak, W.Minor. Crystal Structure of the Staphylococcus Aureus Protein (NP_646141.1, Domain 3912-4037) Similar to Streptococcal Adhesins Emb and Ebha/Ebhb To Be Published.