Zinc in PDB 3ram: Crystal Structure of Hmra

The structure of Crystal Structure of Hmra, PDB code: 3ram was solved by T.Botelho, T.Guevara, A.Marrero, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.52 / 2.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	132.730, 132.730, 336.890, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.8

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

Zinc binding site 1 out of 9 in the Crystal Structure of Hmra


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 Hmra within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn998 b:33.0 occ:1.00 OE1 A:GLU129 2.0 31.6 1.0 NE2 A:HIS341 2.1 32.5 1.0 SG A:CYS93 2.3 32.3 1.0 CD A:GLU129 2.8 30.5 1.0 O2 A:GOL512 2.8 49.7 1.0 OE2 A:GLU129 2.8 29.9 1.0 CE1 A:HIS341 3.1 32.5 1.0 CD2 A:HIS341 3.2 33.9 1.0 ZN A:ZN999 3.3 32.0 1.0 CB A:CYS93 3.4 32.0 1.0 C1 A:GOL512 3.4 53.2 1.0 C2 A:GOL512 3.7 53.2 1.0 OE1 A:GLU128 3.8 34.7 1.0 ND1 A:HIS341 4.2 34.0 1.0 CG A:GLU129 4.2 30.5 1.0 CG A:HIS341 4.3 34.8 1.0 O1 A:GOL512 4.3 53.0 1.0 NE2 A:HIS95 4.4 28.7 1.0 C3 A:GOL512 4.7 54.0 1.0 CA A:CYS93 4.7 33.5 1.0 O2 A:GOL513 4.7 54.0 1.0 CE1 A:HIS95 4.8 27.9 1.0 CD1 A:LEU86 4.8 29.6 1.0 NE2 A:HIS156 5.0 29.2 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Hmra


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 Hmra within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:32.0 occ:1.00 NE2 A:HIS156 2.1 29.2 1.0 NE2 A:HIS95 2.2 28.7 1.0 SG A:CYS93 2.7 32.3 1.0 O2 A:GOL512 2.8 49.7 1.0 CE1 A:HIS156 3.1 29.5 1.0 CD2 A:HIS95 3.1 28.7 1.0 CD2 A:HIS156 3.2 27.9 1.0 CE1 A:HIS95 3.2 27.9 1.0 OE1 A:GLU128 3.2 34.7 1.0 ZN A:ZN998 3.3 33.0 1.0 CB A:CYS93 3.7 32.0 1.0 OE1 A:GLU129 3.8 31.6 1.0 CD A:GLU128 4.0 31.9 1.0 OE1 A:GLU82 4.1 31.7 1.0 O A:CYS93 4.1 31.2 1.0 C2 A:GOL512 4.1 53.2 1.0 ND1 A:HIS156 4.2 29.5 1.0 CG A:HIS95 4.3 27.8 1.0 ND1 A:HIS95 4.3 27.9 1.0 CG A:HIS156 4.3 29.4 1.0 CD1 A:ILE98 4.5 24.4 1.0 CG A:GLU128 4.5 30.0 1.0 CD A:GLU129 4.7 30.5 1.0 C A:CYS93 4.8 32.7 1.0 CA A:CYS93 4.8 33.5 1.0 OE2 A:GLU128 4.9 31.1 1.0 C3 A:GOL513 4.9 52.5 1.0 O3 A:GOL512 5.0 55.0 1.0 C3 A:GOL512 5.0 54.0 1.0 C1 A:GOL512 5.0 53.2 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Hmra


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 Hmra within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn998 b:37.3 occ:1.00 OE1 B:GLU129 2.0 35.2 1.0 NE2 B:HIS341 2.2 36.3 1.0 SG B:CYS93 2.4 32.4 1.0 OE2 B:GLU129 2.6 31.1 1.0 CD B:GLU129 2.7 32.0 1.0 O2 B:GOL530 2.7 52.4 1.0 C1 B:GOL530 3.1 54.2 1.0 CE1 B:HIS341 3.1 36.5 1.0 CD2 B:HIS341 3.1 37.3 1.0 CB B:CYS93 3.4 34.4 1.0 C2 B:GOL530 3.4 55.3 1.0 ZN B:ZN999 3.5 36.5 1.0 OE1 B:GLU128 3.9 33.0 1.0 O1 B:GOL530 4.0 53.6 1.0 CG B:GLU129 4.1 31.2 1.0 ND1 B:HIS341 4.2 37.2 1.0 C3 B:GOL530 4.3 57.5 1.0 CG B:HIS341 4.3 37.6 1.0 O3 B:GOL503 4.4 69.6 1.0 NE2 B:HIS95 4.4 33.8 1.0 CE1 B:HIS95 4.7 33.1 1.0 CA B:CYS93 4.7 35.9 1.0 CD1 B:LEU86 4.9 33.5 1.0 C3 B:GOL503 4.9 69.8 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Hmra


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 Hmra within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn999 b:36.5 occ:1.00 NE2 B:HIS95 2.2 33.8 1.0 NE2 B:HIS156 2.2 33.4 1.0 O2 B:GOL530 2.4 52.4 1.0 SG B:CYS93 2.6 32.4 1.0 CD2 B:HIS156 3.0 32.2 1.0 CD2 B:HIS95 3.1 33.4 1.0 CE1 B:HIS95 3.2 33.1 1.0 CE1 B:HIS156 3.2 34.5 1.0 ZN B:ZN998 3.5 37.3 1.0 OE1 B:GLU128 3.5 33.0 1.0 C2 B:GOL530 3.8 55.3 1.0 OE1 B:GLU129 3.8 35.2 1.0 CB B:CYS93 3.8 34.4 1.0 CD B:GLU128 4.1 30.7 1.0 OE1 B:GLU82 4.2 33.3 1.0 CG B:HIS156 4.2 32.8 1.0 O B:CYS93 4.2 34.5 1.0 ND1 B:HIS95 4.3 32.6 1.0 CG B:HIS95 4.3 33.1 1.0 ND1 B:HIS156 4.3 33.9 1.0 C3 B:GOL530 4.3 57.5 1.0 CD1 B:ILE98 4.5 26.8 1.0 CG B:GLU128 4.5 29.7 1.0 CD B:GLU129 4.7 32.0 1.0 C1 B:GOL530 4.7 54.2 1.0 OE2 B:GLU128 4.8 30.6 1.0 CA B:CYS93 4.9 35.9 1.0 C B:CYS93 4.9 35.9 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Hmra


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 Hmra within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn533 b:81.6 occ:0.50 NE2 B:HIS388 2.6 94.9 1.0 CD2 B:HIS388 3.1 90.2 1.0 CE1 B:HIS388 3.9 95.5 1.0 CG B:HIS388 4.4 87.1 1.0 ND1 B:HIS388 4.8 91.1 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Hmra


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 Hmra within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn998 b:55.0 occ:1.00 OE1 C:GLU129 2.0 53.7 1.0 NE2 C:HIS341 2.2 58.4 1.0 SG C:CYS93 2.3 52.5 1.0 O2 C:GOL531 2.7 74.5 1.0 OE2 C:GLU129 2.7 55.8 1.0 CD C:GLU129 2.7 53.8 1.0 CD2 C:HIS341 3.1 59.9 1.0 CE1 C:HIS341 3.1 59.9 1.0 CB C:CYS93 3.3 54.0 1.0 C1 C:GOL531 3.4 75.4 1.0 ZN C:ZN999 3.4 47.8 1.0 C2 C:GOL531 3.5 75.9 1.0 O1 C:GOL531 4.1 74.3 1.0 CG C:GLU129 4.2 52.3 1.0 C3 C:GOL531 4.2 76.9 1.0 ND1 C:HIS341 4.2 62.6 1.0 OE1 C:GLU128 4.3 51.5 1.0 NE2 C:HIS95 4.3 43.3 1.0 CG C:HIS341 4.3 62.9 1.0 CE1 C:HIS95 4.5 42.3 1.0 CA C:CYS93 4.6 56.3 1.0 CD1 C:LEU86 4.8 62.2 1.0 O C:HOH562 4.8 27.9 1.0 O2 C:GOL508 4.9 71.5 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Hmra


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 Hmra within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn999 b:47.8 occ:1.00 NE2 C:HIS156 2.1 46.3 1.0 NE2 C:HIS95 2.2 43.3 1.0 O2 C:GOL531 2.6 74.5 1.0 SG C:CYS93 2.6 52.5 1.0 CD2 C:HIS156 3.0 43.3 1.0 CE1 C:HIS95 3.1 42.3 1.0 CD2 C:HIS95 3.1 43.7 1.0 CE1 C:HIS156 3.2 47.5 1.0 ZN C:ZN998 3.4 55.0 1.0 CB C:CYS93 3.8 54.0 1.0 C2 C:GOL531 3.9 75.9 1.0 OE1 C:GLU129 3.9 53.7 1.0 OE1 C:GLU128 4.0 51.5 1.0 CD C:GLU128 4.1 46.9 1.0 OE1 C:GLU82 4.1 43.1 1.0 CG C:HIS156 4.2 43.6 1.0 C3 C:GOL531 4.2 76.9 1.0 ND1 C:HIS95 4.2 42.3 1.0 ND1 C:HIS156 4.3 46.4 1.0 CG C:HIS95 4.3 43.9 1.0 O C:CYS93 4.4 52.1 1.0 CD1 C:ILE98 4.4 36.3 1.0 CG C:GLU128 4.5 44.7 1.0 OE2 C:GLU128 4.5 45.2 1.0 CD C:GLU129 4.8 53.8 1.0 O1 C:GOL508 4.9 70.0 1.0 CA C:CYS93 4.9 56.3 1.0 C C:CYS93 4.9 54.5 1.0 C1 C:GOL531 5.0 75.4 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Hmra


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 Hmra within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn998 b:31.9 occ:1.00 OE1 D:GLU129 2.0 29.1 1.0 NE2 D:HIS341 2.2 30.7 1.0 SG D:CYS93 2.3 24.7 1.0 O2 D:GOL504 2.6 41.5 1.0 CD D:GLU129 2.8 27.7 1.0 OE2 D:GLU129 2.9 28.7 1.0 CE1 D:HIS341 3.0 31.5 1.0 C2 D:GOL504 3.0 43.8 1.0 CD2 D:HIS341 3.2 31.1 1.0 CB D:CYS93 3.4 25.0 1.0 ZN D:ZN999 3.4 26.9 1.0 C3 D:GOL504 3.7 43.9 1.0 OE1 D:GLU128 3.8 27.9 1.0 O3 D:GOL504 4.0 44.4 1.0 ND1 D:HIS341 4.2 32.6 1.0 CG D:GLU129 4.3 27.1 1.0 NE2 D:HIS95 4.3 22.1 1.0 CG D:HIS341 4.3 31.7 1.0 C1 D:GOL504 4.4 45.6 1.0 O D:HOH635 4.5 23.4 1.0 CE1 D:HIS95 4.6 21.0 1.0 CA D:CYS93 4.7 25.5 1.0 O D:HOH544 4.7 35.1 1.0 NE2 D:HIS156 5.0 25.4 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Hmra


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 Hmra within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn999 b:26.9 occ:1.00 NE2 D:HIS156 2.1 25.4 1.0 NE2 D:HIS95 2.1 22.1 1.0 O2 D:GOL504 2.5 41.5 1.0 SG D:CYS93 2.8 24.7 1.0 CD2 D:HIS156 3.0 24.4 1.0 CD2 D:HIS95 3.0 21.0 1.0 CE1 D:HIS95 3.2 21.0 1.0 CE1 D:HIS156 3.2 26.6 1.0 OE1 D:GLU128 3.3 27.9 1.0 ZN D:ZN998 3.4 31.9 1.0 CB D:CYS93 3.8 25.0 1.0 C2 D:GOL504 3.8 43.8 1.0 OE1 D:GLU129 3.9 29.1 1.0 CD D:GLU128 4.1 26.8 1.0 OE1 D:GLU82 4.1 28.6 1.0 O D:CYS93 4.2 23.7 1.0 CG D:HIS156 4.2 25.2 1.0 CG D:HIS95 4.2 21.4 1.0 ND1 D:HIS156 4.2 26.1 1.0 ND1 D:HIS95 4.3 21.0 1.0 CD1 D:ILE98 4.4 18.0 1.0 C1 D:GOL504 4.4 45.6 1.0 C1 D:GOL511 4.7 67.6 1.0 CG D:GLU128 4.7 25.9 1.0 C3 D:GOL504 4.7 43.9 1.0 OE2 D:GLU128 4.8 24.8 1.0 CA D:CYS93 4.8 25.5 1.0 C D:CYS93 4.9 24.8 1.0 CD D:GLU129 4.9 27.7 1.0

T.O.Botelho, T.Guevara, A.Marrero, P.Arede, V.S.Fluxa, J.L.Reymond, D.C.Oliveira, F.X.Gomis-Ruth. Structural and Functional Analyses Reveal That Staphylococcus Aureus Antibiotic Resistance Factor Hmra Is A Zinc-Dependent Endopeptidase. J.Biol.Chem. V. 286 25697 2011.
ISSN: ISSN 0021-9258
PubMed: 21622555
DOI: 10.1074/JBC.M111.247437