Zinc in PDB 4h4l: Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn)

The structure of Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn), PDB code: 4h4l was solved by B.Dhakshnamoorthy, T.S.Misono, H.Mizuno, P.K.R.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.28 / 2.50
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	129.530, 129.530, 76.670, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 29.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn) (pdb code 4h4l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn), PDB code: 4h4l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn)


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 Ternary Complex of Hutp(Hutp-L-His-Zn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:47.6 occ:1.00 NE2 A:HIS201 2.1 44.6 1.0 NE2 B:HIS138 2.1 39.2 1.0 NE2 A:HIS73 2.2 50.5 1.0 NE2 A:HIS77 2.2 43.0 1.0 CE1 A:HIS201 2.8 42.2 1.0 CD2 A:HIS73 2.9 50.2 1.0 CE1 A:HIS77 3.0 38.5 1.0 CD2 B:HIS138 3.0 38.3 1.0 CE1 A:HIS73 3.1 45.6 1.0 CD2 A:HIS201 3.2 41.6 1.0 CD2 A:HIS77 3.2 42.0 1.0 CE1 B:HIS138 3.2 39.3 1.0 ND1 A:HIS201 4.0 46.4 1.0 CG A:HIS73 4.1 48.5 1.0 O J:ILE145 4.1 57.0 1.0 ND1 A:HIS73 4.1 47.1 1.0 ND1 A:HIS77 4.2 36.6 1.0 CG A:HIS201 4.2 42.2 1.0 NH1 B:ARG88 4.2 27.9 1.0 CG B:HIS138 4.2 41.4 1.0 ND1 B:HIS138 4.3 39.1 1.0 CG A:HIS77 4.3 39.5 1.0 OE1 J:GLU81 4.4 53.3 1.0 OH A:TYR69 4.8 51.2 1.0 OE2 J:GLU81 4.8 50.3 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn)


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 Ternary Complex of Hutp(Hutp-L-His-Zn) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:50.5 occ:1.00 NE2 B:HIS201 2.1 42.4 1.0 NE2 C:HIS138 2.1 53.2 1.0 NE2 B:HIS77 2.1 43.7 1.0 NE2 B:HIS73 2.1 45.9 1.0 CD2 B:HIS201 2.7 38.5 1.0 CE1 B:HIS77 2.9 39.4 1.0 CD2 C:HIS138 3.0 55.7 1.0 CD2 B:HIS73 3.1 40.3 1.0 CE1 B:HIS73 3.1 41.1 1.0 CE1 C:HIS138 3.1 51.0 1.0 CD2 B:HIS77 3.3 38.1 1.0 CE1 B:HIS201 3.3 37.9 1.0 CG B:HIS201 4.0 36.7 1.0 ND1 B:HIS77 4.2 38.9 1.0 ND1 B:HIS73 4.2 43.8 1.0 O L:ILE145 4.2 47.3 1.0 CG B:HIS73 4.2 39.3 1.0 CG C:HIS138 4.2 54.5 1.0 ND1 C:HIS138 4.2 50.9 1.0 ND1 B:HIS201 4.2 37.7 1.0 NH1 C:ARG88 4.3 26.1 1.0 CG B:HIS77 4.3 42.3 1.0 OE2 L:GLU81 4.7 45.5 1.0 OH B:TYR69 4.7 39.7 1.0 OE1 L:GLU81 4.9 39.4 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn)


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 Ternary Complex of Hutp(Hutp-L-His-Zn) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:48.2 occ:1.00 NE2 C:HIS201 2.0 45.0 1.0 NE2 A:HIS138 2.2 38.9 1.0 NE2 C:HIS77 2.2 41.1 1.0 NE2 C:HIS73 2.2 37.3 1.0 CE1 C:HIS77 2.8 38.8 1.0 CD2 C:HIS201 2.9 46.4 1.0 CD2 A:HIS138 3.0 39.2 1.0 CE1 C:HIS201 3.0 41.2 1.0 CD2 C:HIS73 3.1 37.7 1.0 CE1 C:HIS73 3.1 34.5 1.0 CE1 A:HIS138 3.3 38.3 1.0 CD2 C:HIS77 3.4 37.0 1.0 ND1 C:HIS77 4.1 34.8 1.0 O K:ILE145 4.1 58.3 1.0 CG C:HIS201 4.1 49.7 1.0 ND1 C:HIS201 4.1 49.5 1.0 ND1 C:HIS73 4.1 34.5 1.0 CG C:HIS73 4.2 37.7 1.0 CG A:HIS138 4.2 44.9 1.0 ND1 A:HIS138 4.3 43.5 1.0 CG C:HIS77 4.3 36.8 1.0 OE2 K:GLU81 4.5 58.4 1.0 OH C:TYR69 4.6 48.5 1.0 NH1 A:ARG88 4.7 34.2 1.0 OE1 K:GLU81 4.7 73.8 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn)


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 Ternary Complex of Hutp(Hutp-L-His-Zn) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:46.8 occ:1.00 NE2 D:HIS201 2.0 41.3 1.0 NE2 E:HIS138 2.1 39.4 1.0 NE2 D:HIS73 2.2 49.4 1.0 NE2 D:HIS77 2.2 40.7 1.0 CE1 D:HIS201 2.7 43.3 1.0 CE1 D:HIS77 2.9 39.0 1.0 CD2 D:HIS73 3.1 49.3 1.0 CD2 E:HIS138 3.1 43.0 1.0 CE1 D:HIS73 3.1 43.2 1.0 CE1 E:HIS138 3.1 41.5 1.0 CD2 D:HIS201 3.2 42.2 1.0 CD2 D:HIS77 3.3 39.7 1.0 ND1 D:HIS201 4.0 47.3 1.0 ND1 D:HIS77 4.1 35.9 1.0 ND1 D:HIS73 4.1 45.8 1.0 CG D:HIS73 4.2 49.0 1.0 O G:ILE145 4.2 47.3 1.0 CG D:HIS201 4.2 44.9 1.0 ND1 E:HIS138 4.2 40.9 1.0 CG E:HIS138 4.2 44.0 1.0 NH1 E:ARG88 4.3 28.0 1.0 CG D:HIS77 4.3 37.2 1.0 OE1 G:GLU81 4.6 47.5 1.0 OE2 G:GLU81 4.7 45.4 1.0 OH D:TYR69 4.8 56.2 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn)


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 Ternary Complex of Hutp(Hutp-L-His-Zn) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:48.5 occ:1.00 NE2 F:HIS201 2.1 43.6 1.0 NE2 E:HIS77 2.1 41.7 1.0 NE2 F:HIS138 2.1 50.3 1.0 NE2 E:HIS73 2.1 47.1 1.0 CD2 F:HIS201 2.6 39.4 1.0 CD2 E:HIS73 3.0 44.0 1.0 CE1 E:HIS77 3.0 38.0 1.0 CD2 F:HIS138 3.1 51.7 1.0 CE1 F:HIS138 3.1 44.9 1.0 CE1 E:HIS73 3.1 41.9 1.0 CD2 E:HIS77 3.2 34.3 1.0 CE1 F:HIS201 3.3 39.4 1.0 CG F:HIS201 4.0 38.6 1.0 O I:ILE145 4.1 41.7 1.0 CG E:HIS73 4.1 39.2 1.0 ND1 F:HIS138 4.2 45.5 1.0 ND1 E:HIS73 4.2 42.3 1.0 CG F:HIS138 4.2 49.5 1.0 ND1 E:HIS77 4.2 35.6 1.0 ND1 F:HIS201 4.2 39.4 1.0 NH1 F:ARG88 4.3 23.4 1.0 CG E:HIS77 4.3 36.9 1.0 OH E:TYR69 4.4 41.6 1.0 OE2 I:GLU81 4.7 43.2 1.0 OE1 I:GLU81 4.9 43.4 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn)


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 Ternary Complex of Hutp(Hutp-L-His-Zn) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn202 b:43.4 occ:1.00 NE2 D:HIS203 2.1 45.5 1.0 O H:HOH302 2.1 27.1 1.0 NE2 D:HIS138 2.1 41.9 1.0 NE2 F:HIS73 2.2 39.8 1.0 NE2 F:HIS77 2.2 38.0 1.0 CD2 D:HIS203 2.6 44.2 1.0 CE1 F:HIS77 3.0 36.7 1.0 CD2 F:HIS73 3.0 41.5 1.0 CD2 D:HIS138 3.1 45.0 1.0 CE1 F:HIS73 3.1 35.1 1.0 CE1 D:HIS138 3.1 39.6 1.0 CD2 F:HIS77 3.3 32.8 1.0 CE1 D:HIS203 3.3 41.8 1.0 CG D:HIS203 3.9 47.4 1.0 O H:ILE145 4.1 51.0 1.0 ND1 F:HIS77 4.2 34.0 1.0 ND1 F:HIS73 4.2 36.5 1.0 CG F:HIS73 4.2 37.8 1.0 ND1 D:HIS203 4.2 48.0 1.0 ND1 D:HIS138 4.2 42.5 1.0 CG D:HIS138 4.2 47.5 1.0 CG F:HIS77 4.3 34.9 1.0 OH F:TYR69 4.5 51.3 1.0 NH1 D:ARG88 4.6 39.4 1.0 OE1 H:GLU81 4.7 57.5 1.0 OE2 H:GLU81 4.7 52.4 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn)


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 Ternary Complex of Hutp(Hutp-L-His-Zn) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn202 b:61.3 occ:1.00 NE2 H:HIS138 2.1 53.5 1.0 NE2 G:HIS73 2.2 57.5 1.0 NE2 G:HIS77 2.2 44.3 1.0 NE2 G:HIS201 2.2 77.0 1.0 CD2 G:HIS201 2.2 77.1 1.0 CE1 G:HIS77 2.6 45.7 1.0 CD2 G:HIS73 2.8 60.9 1.0 CD2 H:HIS138 2.8 53.5 1.0 CE1 G:HIS73 3.2 54.8 1.0 CE1 H:HIS138 3.2 48.0 1.0 CD2 G:HIS77 3.4 48.1 1.0 CE1 G:HIS201 3.5 76.6 1.0 CG G:HIS201 3.6 80.7 1.0 ND1 G:HIS77 3.9 48.4 1.0 CG G:HIS73 4.0 61.2 1.0 CG H:HIS138 4.0 52.1 1.0 ND1 G:HIS201 4.1 82.5 1.0 ND1 G:HIS73 4.1 54.4 1.0 ND1 H:HIS138 4.2 47.4 1.0 NH1 H:ARG88 4.3 60.9 1.0 O D:ILE145 4.3 45.5 1.0 CG G:HIS77 4.3 46.1 1.0 OE2 D:GLU81 4.4 63.9 1.0 CB G:HIS201 4.8 80.1 1.0 OH G:TYR69 4.8 66.9 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn)


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 Ternary Complex of Hutp(Hutp-L-His-Zn) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn201 b:46.4 occ:1.00 NE2 I:HIS201 2.1 47.3 1.0 NE2 H:HIS73 2.1 35.7 1.0 NE2 I:HIS138 2.2 41.9 1.0 NE2 H:HIS77 2.2 39.4 1.0 CD2 I:HIS201 2.7 54.3 1.0 CD2 H:HIS73 2.9 34.1 1.0 CD2 I:HIS138 3.1 35.7 1.0 CE1 H:HIS77 3.1 37.5 1.0 CE1 I:HIS138 3.2 38.0 1.0 CD2 H:HIS77 3.2 40.2 1.0 CE1 H:HIS73 3.2 34.0 1.0 CE1 I:HIS201 3.3 42.6 1.0 CG I:HIS201 4.0 55.6 1.0 CG H:HIS73 4.1 38.7 1.0 ND1 H:HIS73 4.2 36.5 1.0 ND1 I:HIS201 4.2 45.8 1.0 ND1 H:HIS77 4.3 42.2 1.0 CG I:HIS138 4.3 37.3 1.0 NH1 I:ARG88 4.3 34.9 1.0 ND1 I:HIS138 4.3 36.8 1.0 CG H:HIS77 4.3 40.9 1.0 O F:ILE145 4.4 30.4 1.0 OE2 F:GLU81 4.6 50.0 1.0 OH H:TYR69 4.6 42.9 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn)


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 Ternary Complex of Hutp(Hutp-L-His-Zn) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:57.0 occ:1.00 NE2 G:HIS203 2.1 42.0 1.0 NE2 I:HIS73 2.1 47.3 1.0 NE2 G:HIS138 2.2 58.9 1.0 NE2 I:HIS77 2.2 59.4 1.0 CD2 G:HIS203 2.4 45.9 1.0 CD2 I:HIS73 3.0 47.3 1.0 CD2 G:HIS138 3.0 56.5 1.0 CE1 I:HIS77 3.1 50.2 1.0 CE1 I:HIS73 3.2 44.2 1.0 CD2 I:HIS77 3.2 50.4 1.0 CE1 G:HIS138 3.2 55.1 1.0 CE1 G:HIS203 3.4 43.8 1.0 CG G:HIS203 3.8 46.7 1.0 CG I:HIS73 4.2 50.1 1.0 ND1 G:HIS203 4.2 48.5 1.0 ND1 I:HIS73 4.2 44.9 1.0 CG G:HIS138 4.2 58.5 1.0 NH1 G:ARG88 4.3 39.8 1.0 ND1 I:HIS77 4.3 52.2 1.0 O E:ILE145 4.3 42.7 1.0 ND1 G:HIS138 4.3 53.1 1.0 CG I:HIS77 4.4 52.1 1.0 OH I:TYR69 4.7 53.5 1.0 OE1 E:GLU81 4.9 64.4 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Ternary Complex of Hutp(Hutp-L-His-Zn)


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 Ternary Complex of Hutp(Hutp-L-His-Zn) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn202 b:60.0 occ:1.00 NE2 K:HIS138 2.1 51.8 1.0 NE2 J:HIS201 2.1 68.5 1.0 NE2 J:HIS73 2.1 64.6 1.0 NE2 J:HIS77 2.2 42.4 1.0 CE1 J:HIS77 2.6 42.9 1.0 CD2 K:HIS138 2.9 53.1 1.0 CD2 J:HIS73 2.9 67.9 1.0 CD2 J:HIS201 3.0 71.0 1.0 CE1 K:HIS138 3.1 52.0 1.0 CE1 J:HIS73 3.1 64.3 1.0 CE1 J:HIS201 3.2 69.6 1.0 CD2 J:HIS77 3.5 45.8 1.0 ND1 J:HIS77 3.9 40.6 1.0 NH1 K:ARG88 3.9 65.7 1.0 CG K:HIS138 4.0 54.4 1.0 CG J:HIS73 4.1 69.3 1.0 O A:ILE145 4.1 48.5 1.0 ND1 K:HIS138 4.1 50.8 1.0 ND1 J:HIS73 4.1 65.3 1.0 CG J:HIS201 4.2 73.3 1.0 ND1 J:HIS201 4.2 72.7 1.0 CG J:HIS77 4.3 43.1 1.0 OE2 A:GLU81 4.3 55.4 1.0 OH J:TYR69 4.7 56.4 1.0 CZ K:ARG88 4.8 61.9 1.0 NH2 K:ARG88 5.0 66.9 1.0

B.Dhakshnamoorthy, H.Mizuno, P.K.R.Kumar. Alternative Binding Modes of L-Histidine Guided By Metal Ions For the Activation of the Antiterminator Protein Hutp of Bacillus Subtilis. J.Struct.Biol. V. 183 512 2013.
ISSN: ISSN 1047-8477
PubMed: 23748184
DOI: 10.1016/J.JSB.2013.05.019