Zinc in PDB 2qq4: Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8

The structure of Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8, PDB code: 2qq4 was solved by J.Jeyakanthan, S.P.Kanaujia, K.Sekar, Y.Agari, A.Ebihara, A.Shinkai, S.Kuramitsu, S.Yokoyama, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.85 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.886, 64.866, 96.260, 71.18, 78.96, 79.02
R / Rfree (%)	22.5 / 26

The binding sites of Zinc atom in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 (pdb code 2qq4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8, PDB code: 2qq4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8


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 Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn139 b:25.0 occ:1.00 OD2 A:ASP41 1.9 29.3 1.0 SG A:CYS125 2.3 21.7 1.0 SG A:CYS64 2.4 20.4 1.0 SG A:CYS39 2.5 66.4 1.0 CG A:ASP41 2.8 31.0 1.0 OD1 A:ASP41 3.0 27.3 1.0 CB A:CYS125 3.1 17.4 1.0 CB A:CYS64 3.4 21.2 1.0 CB A:CYS39 3.7 72.9 1.0 CA A:CYS125 4.0 16.9 1.0 O H:HOH915 4.1 53.7 1.0 CB A:ASP41 4.2 33.9 1.0 N A:CYS64 4.3 23.0 1.0 OG A:SER67 4.4 25.3 1.0 CA A:CYS64 4.4 21.6 1.0 CB A:SER67 4.5 23.2 1.0 OD1 A:ASN36 4.6 34.6 1.0 O A:HOH611 4.6 43.6 1.0 O H:PRO105 4.7 67.9 1.0 N A:CYS125 4.9 16.5 1.0 N A:SER67 5.0 21.7 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8


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 Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn139 b:30.0 occ:1.00 OD2 B:ASP41 1.9 30.0 1.0 SG B:CYS125 2.2 28.6 1.0 SG B:CYS64 2.3 28.2 1.0 SG B:CYS39 2.4 31.8 1.0 CG B:ASP41 2.8 30.5 1.0 CB B:CYS39 3.0 37.9 1.0 OD1 B:ASP41 3.1 28.7 1.0 CB B:CYS125 3.2 24.3 1.0 NH2 B:ARG122 3.3 55.6 1.0 CB B:CYS64 3.4 30.4 1.0 CA B:CYS125 4.0 22.1 1.0 CB B:ASP41 4.2 31.1 1.0 N B:CYS64 4.3 32.1 1.0 ND2 B:ASN36 4.4 54.1 1.0 CA B:CYS39 4.4 40.0 1.0 CA B:CYS64 4.5 29.8 1.0 OD1 B:ASN36 4.6 53.6 1.0 CB B:SER67 4.6 23.5 1.0 CZ B:ARG122 4.6 53.5 1.0 OG B:SER67 4.7 23.8 1.0 CG B:ASN36 4.9 53.9 1.0 N B:CYS125 4.9 23.7 1.0 O D:HOH380 4.9 57.7 1.0 O B:HOH674 5.0 38.2 1.0 C B:CYS39 5.0 39.2 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8


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 Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn139 b:26.6 occ:1.00 OD2 C:ASP41 1.9 23.5 1.0 SG C:CYS39 2.3 33.0 1.0 SG C:CYS125 2.3 26.9 1.0 SG C:CYS64 2.4 23.0 1.0 CG C:ASP41 2.8 29.0 1.0 CB C:CYS39 3.1 37.3 1.0 OD1 C:ASP41 3.1 28.2 1.0 CB C:CYS125 3.2 22.1 1.0 CB C:CYS64 3.3 25.2 1.0 NH2 C:ARG122 3.9 31.2 1.0 ND2 C:ASN36 4.0 39.0 1.0 CA C:CYS125 4.1 23.1 1.0 O G:HOH901 4.1 27.7 1.0 CB C:ASP41 4.2 29.5 1.0 NE C:ARG122 4.2 27.8 1.0 N C:CYS64 4.3 28.1 1.0 CA C:CYS64 4.4 23.3 1.0 OG C:SER67 4.5 21.0 1.0 CZ C:ARG122 4.5 31.0 1.0 CA C:CYS39 4.5 37.0 1.0 CB C:SER67 4.7 20.9 1.0 N C:CYS125 4.9 22.9 1.0 C C:CYS39 4.9 36.2 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8


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 Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn139 b:24.3 occ:1.00 OD2 D:ASP41 1.9 28.7 1.0 SG D:CYS125 2.3 21.1 1.0 SG D:CYS64 2.3 21.2 1.0 SG D:CYS39 2.4 25.8 1.0 CG D:ASP41 2.8 27.3 1.0 CB D:CYS39 3.0 28.3 1.0 OD1 D:ASP41 3.0 24.0 1.0 CB D:CYS125 3.2 21.7 1.0 CB D:CYS64 3.3 17.4 1.0 NE D:ARG122 4.0 26.2 1.0 NH2 D:ARG122 4.1 24.9 1.0 CA D:CYS125 4.1 21.5 1.0 CB D:ASP41 4.2 26.8 1.0 ND2 D:ASN36 4.3 34.1 1.0 N D:CYS64 4.4 17.7 1.0 CA D:CYS64 4.4 18.6 1.0 CA D:CYS39 4.5 31.6 1.0 CZ D:ARG122 4.5 26.0 1.0 CB D:SER67 4.5 21.2 1.0 O D:HOH536 4.6 26.8 1.0 OG D:SER67 4.7 24.9 1.0 C D:CYS39 4.9 31.5 1.0 O C:HOH409 4.9 31.1 1.0 N D:SER67 4.9 19.7 1.0 N D:CYS125 5.0 22.2 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8


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 Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn139 b:28.3 occ:1.00 OD2 E:ASP41 2.1 25.7 1.0 SG E:CYS125 2.2 29.6 1.0 SG E:CYS64 2.4 26.1 1.0 SG E:CYS39 2.4 32.3 1.0 CG E:ASP41 3.0 29.4 1.0 CB E:CYS39 3.0 38.3 1.0 CB E:CYS125 3.1 28.1 1.0 OD1 E:ASP41 3.2 26.4 1.0 CB E:CYS64 3.4 25.8 1.0 CA E:CYS125 4.0 28.1 1.0 NE E:ARG122 4.0 35.0 1.0 NH2 E:ARG122 4.1 37.5 1.0 ND2 E:ASN36 4.3 51.5 1.0 O E:HOH438 4.3 32.4 1.0 CB E:ASP41 4.3 30.1 1.0 N E:CYS64 4.4 27.4 1.0 CA E:CYS39 4.5 41.5 1.0 CA E:CYS64 4.5 25.4 1.0 CZ E:ARG122 4.5 36.2 1.0 CB E:SER67 4.5 25.7 1.0 OG E:SER67 4.8 29.4 1.0 N E:CYS125 4.9 29.4 1.0 O B:HOH244 4.9 22.0 1.0 C E:CYS39 4.9 40.4 1.0 N E:SER67 4.9 24.6 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8


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 Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn139 b:59.2 occ:1.00 OD2 F:ASP41 2.1 36.5 1.0 SG F:CYS125 2.2 46.4 1.0 SG F:CYS64 2.3 38.9 1.0 SG F:CYS39 2.4 74.0 1.0 CG F:ASP41 3.0 44.6 1.0 CB F:CYS39 3.1 77.9 1.0 CB F:CYS125 3.2 43.3 1.0 CB F:CYS64 3.2 42.7 1.0 OD1 F:ASP41 3.3 41.0 1.0 NH2 F:ARG122 3.8 56.6 1.0 NE F:ARG122 3.9 56.5 1.0 CA F:CYS125 4.1 41.4 1.0 CZ F:ARG122 4.3 56.6 1.0 N F:CYS64 4.4 47.4 1.0 CA F:CYS64 4.4 43.0 1.0 CB F:ASP41 4.4 50.4 1.0 ND2 F:ASN36 4.6 91.7 1.0 CA F:CYS39 4.6 78.0 1.0 OG F:SER67 4.8 45.2 1.0 N F:CYS125 4.9 42.5 1.0 CD F:ARG122 5.0 58.0 1.0 CB F:SER67 5.0 40.0 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8


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 Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn139 b:28.3 occ:1.00 OD2 G:ASP41 1.9 30.9 1.0 SG G:CYS125 2.2 34.5 1.0 SG G:CYS39 2.3 32.7 1.0 SG G:CYS64 2.3 27.1 1.0 CG G:ASP41 2.8 32.2 1.0 OD1 G:ASP41 3.0 30.2 1.0 CB G:CYS39 3.1 35.9 1.0 CB G:CYS125 3.2 29.5 1.0 CB G:CYS64 3.4 29.4 1.0 ND2 G:ASN36 4.1 47.6 1.0 NH2 G:ARG122 4.1 34.8 1.0 CA G:CYS125 4.1 29.1 1.0 CB G:ASP41 4.2 33.2 1.0 N G:CYS64 4.3 29.1 1.0 NE G:ARG122 4.3 36.4 1.0 CA G:CYS64 4.5 29.6 1.0 CA G:CYS39 4.6 36.4 1.0 CB G:SER67 4.6 29.6 1.0 CZ G:ARG122 4.7 34.4 1.0 O G:HOH606 4.8 39.8 1.0 OG G:SER67 4.9 34.1 1.0 C G:CYS39 4.9 37.0 1.0 O E:HOH455 5.0 30.4 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8


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 Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn139 b:35.1 occ:1.00 OD2 H:ASP41 1.9 44.5 1.0 SG H:CYS125 2.1 38.0 1.0 SG H:CYS64 2.3 32.9 1.0 SG H:CYS39 2.4 36.3 1.0 CG H:ASP41 2.8 40.9 1.0 OD1 H:ASP41 3.0 40.5 1.0 CB H:CYS39 3.1 41.0 1.0 CB H:CYS125 3.1 34.4 1.0 CB H:CYS64 3.3 34.2 1.0 CA H:CYS125 4.0 33.8 1.0 ND2 H:ASN36 4.0 46.3 1.0 NH2 H:ARG122 4.1 45.3 1.0 CB H:ASP41 4.2 43.3 1.0 N H:CYS64 4.2 36.3 1.0 NE H:ARG122 4.3 44.3 1.0 CA H:CYS64 4.4 35.7 1.0 CA H:CYS39 4.6 42.2 1.0 CB H:SER67 4.6 26.9 1.0 OG H:SER67 4.7 28.3 1.0 CZ H:ARG122 4.7 46.7 1.0 N H:CYS125 4.9 33.8 1.0 C H:CYS39 4.9 42.2 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8


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 Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn139 b:92.6 occ:1.00 OD2 I:ASP41 1.9 46.0 1.0 SG I:CYS125 1.9 38.9 1.0 SG I:CYS39 2.3 51.5 1.0 SG I:CYS64 2.3 39.3 1.0 OD1 I:ASP41 2.4 41.0 1.0 CG I:ASP41 2.5 45.5 1.0 CB I:CYS39 3.1 56.9 1.0 CB I:CYS125 3.4 39.7 1.0 CB I:CYS64 3.4 34.9 1.0 CB I:ASP41 4.0 49.8 1.0 N I:CYS64 4.0 35.8 1.0 CA I:CYS125 4.1 40.2 1.0 NH2 I:ARG122 4.1 62.4 1.0 CA I:CYS64 4.4 36.5 1.0 CB I:SER67 4.5 31.9 1.0 OG I:SER67 4.5 35.7 1.0 CA I:CYS39 4.5 59.8 1.0 NH1 I:ARG122 4.5 64.0 1.0 CZ I:ARG122 4.7 62.4 1.0 N I:ASP41 4.8 56.9 1.0 C I:CYS39 4.9 59.9 1.0 CA I:ASP41 4.9 53.9 1.0 N I:CYS125 4.9 41.4 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8


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 Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn139 b:36.6 occ:1.00 OD2 J:ASP41 1.9 36.3 1.0 SG J:CYS64 2.3 38.7 1.0 SG J:CYS125 2.4 37.9 1.0 SG J:CYS39 2.4 49.2 1.0 CG J:ASP41 2.7 41.3 1.0 CB J:CYS39 2.9 53.8 1.0 OD1 J:ASP41 2.9 37.9 1.0 CB J:CYS125 3.3 36.3 1.0 CB J:CYS64 3.4 38.7 1.0 NE J:ARG122 4.1 37.8 1.0 CB J:ASP41 4.2 45.9 1.0 CA J:CYS125 4.2 36.3 1.0 NH2 J:ARG122 4.2 35.5 1.0 N J:CYS64 4.3 39.3 1.0 CA J:CYS39 4.3 55.7 1.0 CA J:CYS64 4.4 38.0 1.0 CB J:SER67 4.6 40.8 1.0 CZ J:ARG122 4.6 39.2 1.0 OD1 J:ASN36 4.7 78.2 1.0 C J:CYS39 4.8 55.6 1.0

J.Jeyakanthan, S.P.Kanaujia, K.Sekar, Y.Agari, A.Ebihara, A.Shinkai, S.Kuramitsu, S.Yokoyama. Crystal Structure of Iron-Sulfur Cluster Biosynthesis Protein Iscu (TTHA1736) From Thermus Thermophilus HB8 To Be Published.