Zinc in PDB 5tdc: Crystal Structure of the Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide.

The structure of Crystal Structure of the Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide., PDB code: 5tdc was solved by G.Kozlov, J.Munoz-Escobar, E.Matta-Camacho, K.Gehring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.74 / 1.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.274, 49.036, 53.634, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 18

The binding sites of Zinc atom in the Crystal Structure of the Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide. (pdb code 5tdc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide., PDB code: 5tdc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide.


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 Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:14.6 occ:1.00 SG A:CYS124 2.3 14.2 1.0 SG A:CYS99 2.3 17.6 1.0 SG A:CYS149 2.3 12.9 1.0 SG A:CYS127 2.5 14.1 1.0 HB2 A:CYS127 3.0 17.8 1.0 CB A:CYS99 3.2 14.8 1.0 HB3 A:CYS99 3.2 17.8 1.0 HB2 A:CYS99 3.2 17.8 1.0 CB A:CYS149 3.2 11.5 1.0 HB3 A:CYS149 3.2 13.8 1.0 HB2 A:CYS149 3.2 13.8 1.0 H A:CYS124 3.2 16.0 1.0 HB3 A:CYS124 3.3 16.7 1.0 CB A:CYS127 3.4 14.8 1.0 CB A:CYS124 3.4 13.9 1.0 HE3 C:MET140 3.6 29.4 1.0 HB3 A:CYS151 3.6 16.7 1.0 HE1 A:HIS166 3.7 21.2 1.0 HB2 A:CYS151 3.7 16.7 1.0 H A:CYS127 3.8 22.5 1.0 HB3 A:ARG101 3.9 24.8 1.0 HB3 A:CYS127 3.9 17.8 1.0 N A:CYS124 4.0 13.3 1.0 CB A:CYS151 4.1 13.9 1.0 HB2 A:CYS124 4.2 16.7 1.0 HE1 C:MET140 4.2 29.4 1.0 CE C:MET140 4.2 24.5 1.0 CA A:CYS124 4.3 13.8 1.0 H A:ARG101 4.3 26.6 1.0 HE2 C:MET140 4.4 29.4 1.0 H A:CYS151 4.4 15.6 1.0 ZN A:ZN202 4.4 15.5 1.0 HD3 A:ARG101 4.4 33.7 1.0 CE1 A:HIS166 4.4 17.7 1.0 N A:CYS127 4.5 18.8 1.0 CA A:CYS127 4.5 15.9 1.0 HB2 A:ARG101 4.6 24.8 1.0 CA A:CYS99 4.6 21.9 1.0 CA A:CYS149 4.7 10.5 1.0 CB A:ARG101 4.7 20.7 1.0 HA A:LEU123 4.7 15.2 1.0 HD2 A:ARG101 4.7 33.7 1.0 HH21 A:ARG101 4.8 36.7 1.0 HA A:CYS99 4.9 26.2 1.0 HB2 A:ASP126 4.9 21.6 1.0 C A:CYS124 4.9 15.8 1.0 HA A:CYS127 4.9 19.1 1.0 ND1 A:HIS166 4.9 19.1 1.0 O A:CYS124 4.9 13.4 1.0 HA A:CYS149 5.0 12.6 1.0 H A:GLY100 5.0 24.2 1.0 CD A:ARG101 5.0 28.1 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide.


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 Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:15.5 occ:1.00 ND1 A:HIS166 2.1 19.1 1.0 SG A:CYS151 2.3 19.4 1.0 SG A:CYS127 2.3 14.1 1.0 SG A:CYS163 2.3 15.6 1.0 CE1 A:HIS166 2.9 17.7 1.0 HB2 A:HIS166 3.0 24.3 1.0 HB3 A:CYS127 3.0 17.8 1.0 HE1 A:HIS166 3.1 21.2 1.0 CG A:HIS166 3.1 19.3 1.0 HB3 A:CYS151 3.2 16.7 1.0 HB3 A:CYS163 3.2 16.6 1.0 CB A:CYS151 3.2 13.9 1.0 CB A:CYS127 3.2 14.8 1.0 H A:CYS163 3.3 23.2 1.0 HB2 A:CYS151 3.3 16.7 1.0 CB A:CYS163 3.4 13.8 1.0 HA A:CYS127 3.5 19.1 1.0 CB A:HIS166 3.6 20.3 1.0 HB2 A:CYS99 3.6 17.8 1.0 HB2 A:ASN165 3.7 17.9 1.0 H A:HIS166 3.8 21.9 1.0 CA A:CYS127 4.0 15.9 1.0 HB2 A:CYS127 4.0 17.8 1.0 N A:CYS163 4.0 19.3 1.0 NE2 A:HIS166 4.1 20.5 1.0 HB2 A:CYS163 4.1 16.6 1.0 CD2 A:HIS166 4.2 20.4 1.0 HB3 A:HIS166 4.2 24.3 1.0 CA A:CYS163 4.2 14.0 1.0 N A:HIS166 4.3 18.2 1.0 HD22 A:ASN165 4.3 23.8 1.0 ZN A:ZN201 4.4 14.6 1.0 CB A:CYS99 4.5 14.8 1.0 CA A:CYS151 4.6 13.1 1.0 CA A:HIS166 4.6 17.7 1.0 CB A:ASN165 4.7 14.9 1.0 H A:ASN165 4.7 19.9 1.0 C A:CYS163 4.8 14.6 1.0 HB3 A:CYS99 4.9 17.8 1.0 HE2 A:HIS166 4.9 24.6 1.0 HA A:CYS151 4.9 15.7 1.0 O A:CYS163 4.9 17.8 1.0 HA A:PHE162 4.9 16.8 1.0 N A:CYS127 4.9 18.8 1.0 C A:CYS127 5.0 16.7 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide.


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 Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:17.3 occ:1.00 ND1 A:HIS136 2.0 19.4 1.0 ND1 A:HIS133 2.1 15.7 1.0 SG A:CYS112 2.3 16.3 1.0 SG A:CYS115 2.3 17.7 1.0 HB2 A:CYS115 2.8 18.4 1.0 CE1 A:HIS133 2.9 17.6 1.0 CE1 A:HIS136 2.9 16.6 1.0 HE1 A:HIS133 2.9 21.2 1.0 HE1 A:HIS136 3.0 19.9 1.0 CG A:HIS136 3.1 18.4 1.0 CB A:CYS115 3.1 15.4 1.0 CG A:HIS133 3.2 15.1 1.0 HB2 A:HIS136 3.2 20.0 1.0 HA A:HIS133 3.2 16.2 1.0 CB A:CYS112 3.3 17.9 1.0 HB3 A:CYS112 3.3 21.5 1.0 HB3 A:HIS133 3.4 20.1 1.0 HB2 A:CYS112 3.4 21.5 1.0 HB2 A:ASP114 3.4 27.2 1.0 HB3 A:HIS136 3.4 20.0 1.0 CB A:HIS136 3.5 16.7 1.0 H A:CYS115 3.6 21.2 1.0 CB A:HIS133 3.7 16.7 1.0 HB3 A:CYS115 3.8 18.4 1.0 N A:CYS115 3.9 17.7 1.0 CA A:HIS133 3.9 13.5 1.0 HG23 A:VAL132 4.0 19.3 1.0 HG1 A:THR159 4.0 24.4 1.0 NE2 A:HIS133 4.1 19.4 1.0 NE2 A:HIS136 4.1 19.2 1.0 CA A:CYS115 4.1 17.9 1.0 CD2 A:HIS136 4.2 20.3 1.0 CD2 A:HIS133 4.2 17.7 1.0 CB A:ASP114 4.4 22.7 1.0 H A:ASP114 4.5 25.8 1.0 OG1 A:THR159 4.6 20.3 1.0 HB3 A:ASP114 4.6 27.2 1.0 HB2 A:HIS133 4.6 20.1 1.0 CA A:CYS112 4.7 15.1 1.0 HA A:CYS115 4.7 21.4 1.0 C A:ASP114 4.7 20.5 1.0 N A:HIS133 4.7 15.2 1.0 HE2 A:HIS133 4.8 23.2 1.0 HE2 A:HIS136 4.8 23.0 1.0 CG2 A:VAL132 4.9 16.1 1.0 HA A:CYS112 4.9 18.1 1.0 CA A:ASP114 5.0 21.9 1.0 O A:HIS133 5.0 20.8 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide.


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 Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:16.2 occ:1.00 SG C:CYS99 2.3 20.0 1.0 SG C:CYS149 2.3 14.4 1.0 SG C:CYS127 2.4 16.2 1.0 SG C:CYS124 2.4 17.1 1.0 HB2 C:CYS127 3.0 18.7 1.0 HB2 C:CYS99 3.1 22.2 1.0 CB C:CYS149 3.2 15.4 1.0 CB C:CYS99 3.2 18.5 1.0 HB2 C:CYS149 3.2 18.5 1.0 HB3 C:CYS149 3.2 18.5 1.0 H C:CYS124 3.3 16.2 1.0 CB C:CYS127 3.3 15.6 1.0 HB3 C:CYS124 3.3 18.0 1.0 HB3 C:CYS99 3.3 22.2 1.0 CB C:CYS124 3.5 15.0 1.0 HB2 C:CYS151 3.7 19.7 1.0 HB3 C:CYS151 3.7 19.7 1.0 HB3 C:ARG101 3.8 23.9 1.0 H C:CYS127 3.8 19.1 1.0 HB3 C:CYS127 3.9 18.7 1.0 N C:CYS124 4.0 13.5 1.0 CB C:CYS151 4.1 16.4 1.0 HE1 C:HIS166 4.2 28.3 1.0 HB2 C:CYS124 4.2 18.0 1.0 CA C:CYS124 4.3 17.0 1.0 H C:ARG101 4.4 26.1 1.0 H C:CYS151 4.4 17.4 1.0 ZN C:ZN202 4.4 17.6 1.0 N C:CYS127 4.4 15.9 1.0 HB2 C:ARG101 4.4 23.9 1.0 CA C:CYS127 4.5 13.2 1.0 CB C:ARG101 4.6 19.9 1.0 CA C:CYS99 4.6 29.1 1.0 CA C:CYS149 4.7 11.4 1.0 HA C:LEU123 4.7 15.8 1.0 HA C:CYS99 4.8 34.9 1.0 HD3 C:ARG101 4.8 42.5 1.0 CE1 C:HIS166 4.8 23.6 1.0 O C:CYS124 4.9 15.7 1.0 C C:CYS124 4.9 14.7 1.0 HA C:CYS127 4.9 15.9 1.0 HA C:CYS149 4.9 13.7 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide.


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 Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:17.6 occ:1.00 ND1 C:HIS166 2.0 18.7 1.0 SG C:CYS151 2.3 17.7 1.0 SG C:CYS163 2.3 16.6 1.0 SG C:CYS127 2.4 16.2 1.0 HB2 C:HIS166 2.9 24.3 1.0 CE1 C:HIS166 2.9 23.6 1.0 HE1 C:HIS166 3.1 28.3 1.0 HB3 C:CYS127 3.1 18.7 1.0 CG C:HIS166 3.1 22.9 1.0 HB3 C:CYS163 3.2 19.1 1.0 CB C:CYS151 3.3 16.4 1.0 H C:CYS163 3.3 17.8 1.0 HB2 C:CYS151 3.3 19.7 1.0 CB C:CYS127 3.3 15.6 1.0 HB3 C:CYS151 3.3 19.7 1.0 HB2 C:CYS99 3.4 22.2 1.0 CB C:CYS163 3.4 15.9 1.0 CB C:HIS166 3.5 20.3 1.0 HA C:CYS127 3.6 15.9 1.0 N C:CYS163 4.0 14.9 1.0 H C:HIS166 4.0 21.9 1.0 CA C:CYS127 4.1 13.2 1.0 HB3 C:HIS166 4.1 24.3 1.0 NE2 C:HIS166 4.1 29.9 1.0 HB2 C:CYS163 4.1 19.1 1.0 HB2 C:CYS127 4.1 18.7 1.0 O C:HOH321 4.2 26.1 1.0 CD2 C:HIS166 4.2 28.2 1.0 CA C:CYS163 4.3 12.2 1.0 CB C:CYS99 4.3 18.5 1.0 ZN C:ZN201 4.4 16.2 1.0 N C:HIS166 4.6 18.2 1.0 CA C:HIS166 4.7 19.1 1.0 CA C:CYS151 4.7 13.7 1.0 HB3 C:ASN165 4.7 34.4 1.0 HB3 C:CYS99 4.7 22.2 1.0 HA C:PHE162 4.8 20.2 1.0 HD22 C:ASN165 4.8 60.0 1.0 HE2 C:HIS166 4.9 36.0 1.0 C C:CYS163 4.9 15.8 1.0 HA C:CYS151 4.9 16.5 1.0 H C:CYS99 5.0 47.1 1.0 N C:CYS127 5.0 15.9 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide.


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 Human Ubr-Box Domain From UBR1 in Complex with Monomethylated Arginine Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:14.4 occ:1.00 ND1 C:HIS136 2.0 13.8 1.0 ND1 C:HIS133 2.1 13.6 1.0 SG C:CYS112 2.3 14.4 1.0 SG C:CYS115 2.3 14.4 1.0 HB2 C:CYS115 2.8 17.0 1.0 CE1 C:HIS136 2.9 15.8 1.0 CE1 C:HIS133 2.9 14.4 1.0 HE1 C:HIS136 3.0 19.0 1.0 HE1 C:HIS133 3.0 17.3 1.0 CB C:CYS115 3.1 14.2 1.0 CG C:HIS136 3.2 12.0 1.0 CG C:HIS133 3.2 12.9 1.0 HA C:HIS133 3.2 12.7 1.0 HB2 C:HIS136 3.3 17.2 1.0 HB3 C:HIS133 3.3 16.8 1.0 CB C:CYS112 3.3 14.2 1.0 HB2 C:CYS112 3.4 17.0 1.0 HB3 C:CYS112 3.4 17.0 1.0 HB2 C:ASP114 3.5 16.7 1.0 H C:CYS115 3.5 14.9 1.0 CB C:HIS136 3.6 14.4 1.0 HB3 C:HIS136 3.6 17.2 1.0 CB C:HIS133 3.6 14.0 1.0 HB3 C:CYS115 3.8 17.0 1.0 N C:CYS115 3.9 12.4 1.0 CA C:HIS133 3.9 10.6 1.0 HG1 C:THR159 3.9 22.4 1.0 HG23 C:VAL132 4.0 20.3 1.0 NE2 C:HIS136 4.1 14.3 1.0 NE2 C:HIS133 4.1 13.3 1.0 CA C:CYS115 4.1 13.1 1.0 CD2 C:HIS136 4.2 13.7 1.0 CD2 C:HIS133 4.2 14.4 1.0 CB C:ASP114 4.4 13.9 1.0 OG1 C:THR159 4.4 18.7 1.0 H C:ASP114 4.5 21.7 1.0 HB2 C:HIS133 4.5 16.8 1.0 HB3 C:ASP114 4.6 16.7 1.0 HA C:CYS115 4.6 15.7 1.0 C C:ASP114 4.6 16.8 1.0 N C:HIS133 4.7 12.7 1.0 CA C:CYS112 4.7 13.9 1.0 HE2 C:HIS136 4.8 17.2 1.0 HE2 C:HIS133 4.8 16.0 1.0 CG2 C:VAL132 4.9 16.9 1.0 CA C:ASP114 4.9 14.4 1.0 O C:HIS133 4.9 15.7 1.0 HA C:CYS112 4.9 16.7 1.0 C C:HIS133 5.0 14.1 1.0 HG21 C:VAL132 5.0 20.3 1.0

J.Munoz-Escobar, E.Matta-Camacho, C.Cho, G.Kozlov, K.Gehring. Bound Waters Mediate Binding of Diverse Substrates to A Ubiquitin Ligase. Structure V. 25 719 2017.
ISSN: ISSN 1878-4186
PubMed: 28392261
DOI: 10.1016/J.STR.2017.03.004