Zinc in PDB 7q5n: Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex

The structure of Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex, PDB code: 7q5n was solved by K.E.Ravichandran, P.Wilk, P.Grudnik, S.Glatt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.47 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	185.43, 197.22, 139.18, 90, 90, 90
R / Rfree (%)	23.4 / 27.2

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 - 41;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex (pdb code 7q5n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 41 binding sites of Zinc where determined in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex, PDB code: 7q5n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 41 in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex


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 Chaetomium Thermophilum AHP1-URM1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:163.1 occ:1.00 O A:HOH329 2.0 129.6 1.0 O A:HOH309 2.1 114.3 1.0 O A:HOH301 2.4 123.6 1.0 OD1 A:ASP81 3.0 103.8 1.0 OD2 A:ASP81 3.2 90.2 1.0 CG A:ASP81 3.5 87.0 1.0 O A:GLY79 3.8 84.7 1.0 C A:GLY79 4.8 92.8 1.0 CA A:GLY79 5.0 89.3 1.0 CB A:ASP81 5.0 81.7 1.0

Zinc binding site 2 out of 41 in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex


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 Chaetomium Thermophilum AHP1-URM1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:64.9 occ:0.30 CG2 B:VAL93 3.3 57.2 1.0 ND2 A:ASN89 3.3 61.6 1.0 ND2 B:ASN89 3.4 55.6 1.0 CG1 B:VAL93 3.7 52.1 1.0 CB B:VAL93 3.8 76.8 1.0 CG2 A:VAL93 3.9 57.1 1.0 CB B:ASN89 4.0 71.2 1.0 CG1 A:VAL93 4.1 59.9 1.0 CG B:ASN89 4.1 63.8 1.0 CA B:ASN89 4.2 65.7 1.0 CG A:ASN89 4.4 72.4 1.0 CB A:VAL93 4.4 71.2 1.0 N B:ASP90 4.5 72.3 1.0 CB A:ASN89 4.5 71.1 1.0 OD2 B:ASP90 4.7 69.1 1.0 CA A:ASN89 4.8 62.1 1.0 O A:HOH320 4.9 76.8 1.0 C B:ASN89 4.9 75.6 1.0

Zinc binding site 3 out of 41 in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex


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 Chaetomium Thermophilum AHP1-URM1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:165.1 occ:1.00 O B:PRO3 3.4 107.9 1.0 OD2 B:ASP8 3.5 85.2 1.0 CG B:ASP8 4.3 83.5 1.0 OD1 B:ASP8 4.3 89.9 1.0 CG B:GLN5 4.6 96.8 1.0 C B:PRO3 4.6 104.7 1.0 CB B:GLN5 4.8 80.9 1.0 N B:GLN5 5.0 84.5 1.0 CB B:ALA2 5.0 146.7 1.0

Zinc binding site 4 out of 41 in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex


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 Chaetomium Thermophilum AHP1-URM1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:204.9 occ:1.00 OG1 B:THR28 2.4 132.7 1.0 OD1 C:ASP26 3.0 102.9 0.8 CG2 B:THR28 3.0 104.5 1.0 OD1 B:ASP26 3.1 125.8 1.0 CB B:THR28 3.2 119.4 1.0 OD2 B:ASP26 3.9 113.3 1.0 CG B:ASP26 3.9 114.4 1.0 CG C:ASP26 3.9 101.3 0.1 OD2 C:ASP26 4.1 106.4 0.5 CA B:THR28 4.5 117.5 1.0 N B:THR28 4.6 112.1 1.0 O A:ALA100 4.9 72.5 1.0

Zinc binding site 5 out of 41 in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex


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 Chaetomium Thermophilum AHP1-URM1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:189.1 occ:1.00 OD2 C:ASP81 3.3 113.1 1.0 OD1 C:ASP81 3.3 112.4 1.0 CG C:ASP81 3.7 112.0 1.0 O C:GLY79 4.2 98.6 1.0

Zinc binding site 6 out of 41 in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex


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 Chaetomium Thermophilum AHP1-URM1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:165.8 occ:1.00 O I:HOH405 2.3 95.2 1.0 OE1 C:GLU155 3.5 130.2 1.0 OE2 C:GLU155 3.7 124.1 1.0 CD C:GLU155 4.0 128.8 1.0 OD1 I:ASP26 4.4 117.1 0.8

Zinc binding site 7 out of 41 in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex


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 Chaetomium Thermophilum AHP1-URM1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:155.8 occ:0.63 OD1 C:ASP8 3.5 129.1 1.0 OE1 C:GLN5 3.9 141.7 1.0 OD2 C:ASP8 4.2 139.1 1.0 CG C:ASP8 4.2 130.4 1.0

Zinc binding site 8 out of 41 in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex


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 Chaetomium Thermophilum AHP1-URM1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:155.2 occ:0.56 OE2 B:GLU106 2.2 133.2 1.0 NE2 D:GLN74 2.8 149.1 1.0 CD B:GLU106 3.1 134.8 1.0 OD1 D:ASP73 3.1 147.4 1.0 OD2 D:ASP73 3.1 162.9 1.0 CG B:GLU106 3.2 116.3 1.0 CG D:ASP73 3.4 155.9 1.0 O D:ALA70 3.9 106.9 1.0 CD D:GLN74 4.1 148.0 1.0 OE1 B:GLU106 4.2 118.0 1.0 CB B:GLU106 4.4 95.7 1.0 CG D:GLN74 4.7 147.5 1.0 CB D:ASP73 4.9 152.7 1.0 N B:GLU106 5.0 94.9 1.0 CG D:LYS71 5.0 134.5 1.0 CA D:LYS71 5.0 125.0 1.0

Zinc binding site 9 out of 41 in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex


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 Chaetomium Thermophilum AHP1-URM1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:202.6 occ:1.00 OD1 D:ASP81 3.2 157.6 1.0 O D:HOH407 3.2 144.2 1.0 O D:GLY79 3.9 147.2 1.0 CG D:ASP81 4.2 148.6 1.0 OD2 D:ASP81 4.3 153.2 1.0 CA D:GLY79 4.7 138.5 1.0 C D:GLY79 4.7 141.0 1.0

Zinc binding site 10 out of 41 in the Crystal Structure of Chaetomium Thermophilum AHP1-URM1 Complex


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 Chaetomium Thermophilum AHP1-URM1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:186.4 occ:1.00 O E:HOH313 2.0 138.6 1.0 OD1 E:ASP81 2.7 140.0 1.0 OD2 E:ASP81 3.1 132.8 1.0 CG E:ASP81 3.2 135.1 1.0 O E:GLY79 3.8 131.2 1.0 OG1 E:THR46 4.7 133.8 1.0 CB E:ASP81 4.7 125.2 1.0 C E:GLY79 4.8 123.9 1.0

K.E.Ravichandran, L.Kaduhr, B.Skupien-Rabian, E.Shvetsova, M.Sokolowski, R.C.Krutyholowa, D.Kwasna, C.Brachmann, S.Lin, S.Guzman Perez, P.Wilk, M.Kosters, P.Grudnik, U.Jankowska, S.A.Leidel, R.Schaffrath, S.Glatt. E2/E3-Independent Ubiquitin-Like Protein Conjugation By URM1 Is Directly Coupled to Cysteine Persulfidation. Embo J. V. 41 11318 2022.
ISSN: ESSN 1460-2075
PubMed: 36102610
DOI: 10.15252/EMBJ.2022111318