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Zinc in PDB 6egn: Crystal Structure of A Three-Stranded Coiled Coil Peptide Containing A Trigonal Planar Hg(II)S3 Site Modified By D-Leu in the Second Coordination Sphere

Protein crystallography data

The structure of Crystal Structure of A Three-Stranded Coiled Coil Peptide Containing A Trigonal Planar Hg(II)S3 Site Modified By D-Leu in the Second Coordination Sphere, PDB code: 6egn was solved by L.Ruckthong, J.A.Stuckey, V.L.Pecoraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.14 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 32.636, 80.508, 88.730, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 20.9

Other elements in 6egn:

The structure of Crystal Structure of A Three-Stranded Coiled Coil Peptide Containing A Trigonal Planar Hg(II)S3 Site Modified By D-Leu in the Second Coordination Sphere also contains other interesting chemical elements:

Mercury (Hg) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Three-Stranded Coiled Coil Peptide Containing A Trigonal Planar Hg(II)S3 Site Modified By D-Leu in the Second Coordination Sphere (pdb code 6egn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of A Three-Stranded Coiled Coil Peptide Containing A Trigonal Planar Hg(II)S3 Site Modified By D-Leu in the Second Coordination Sphere, PDB code: 6egn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6egn

Go back to Zinc Binding Sites List in 6egn
Zinc binding site 1 out of 3 in the Crystal Structure of A Three-Stranded Coiled Coil Peptide Containing A Trigonal Planar Hg(II)S3 Site Modified By D-Leu in the Second Coordination Sphere


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 A Three-Stranded Coiled Coil Peptide Containing A Trigonal Planar Hg(II)S3 Site Modified By D-Leu in the Second Coordination Sphere within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:27.2
occ:0.90
OE1 A:GLU3 2.0 30.1 0.8
CD A:GLU3 2.8 33.4 0.8
OE2 A:GLU3 2.9 35.6 0.8
CH3 A:ACE0 3.7 46.6 1.0
C A:ACE0 4.2 43.9 1.0
CG A:GLU3 4.2 40.0 0.8
N A:TRP2 4.3 33.2 1.0
N A:GLU3 4.4 35.2 1.0
N A:GLU1 4.5 41.9 1.0
CB A:TRP2 4.5 29.1 1.0
CA A:TRP2 4.8 32.0 1.0
CB A:GLU3 4.9 39.7 1.0
O A:ACE0 4.9 44.4 1.0

Zinc binding site 2 out of 3 in 6egn

Go back to Zinc Binding Sites List in 6egn
Zinc binding site 2 out of 3 in the Crystal Structure of A Three-Stranded Coiled Coil Peptide Containing A Trigonal Planar Hg(II)S3 Site Modified By D-Leu in the Second Coordination Sphere


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 A Three-Stranded Coiled Coil Peptide Containing A Trigonal Planar Hg(II)S3 Site Modified By D-Leu in the Second Coordination Sphere within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:30.4
occ:1.00
NE2 B:HIS35 2.0 29.9 1.0
OE1 B:GLU31 2.0 28.1 1.0
OE2 B:GLU34 2.0 30.9 1.0
CD B:GLU31 2.8 40.4 1.0
CD2 B:HIS35 2.9 30.5 1.0
CD B:GLU34 3.0 39.1 1.0
OE2 B:GLU31 3.0 31.4 1.0
CE1 B:HIS35 3.0 29.7 1.0
CG B:GLU34 3.4 33.8 1.0
NZ C:LYS29 4.0 29.0 0.5
CG B:HIS35 4.1 28.6 1.0
OE1 B:GLU34 4.1 39.5 1.0
ND1 B:HIS35 4.1 30.6 1.0
CG B:GLU31 4.2 29.9 1.0
NZ C:LYS29 4.6 68.0 0.5
CA B:GLU31 4.6 24.0 1.0
CB B:GLU31 4.7 26.3 1.0
CE C:LYS29 4.7 62.5 0.5
O C:HOH224 4.8 59.8 1.0
O B:HOH246 4.9 59.5 1.0
O B:GLU31 4.9 28.7 1.0
CB B:GLU34 4.9 26.4 1.0
CE C:LYS29 5.0 27.9 0.5

Zinc binding site 3 out of 3 in 6egn

Go back to Zinc Binding Sites List in 6egn
Zinc binding site 3 out of 3 in the Crystal Structure of A Three-Stranded Coiled Coil Peptide Containing A Trigonal Planar Hg(II)S3 Site Modified By D-Leu in the Second Coordination Sphere


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 A Three-Stranded Coiled Coil Peptide Containing A Trigonal Planar Hg(II)S3 Site Modified By D-Leu in the Second Coordination Sphere within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:33.1
occ:0.80
O C:HOH207 1.8 36.9 1.0
ND1 C:HIS35 2.0 31.4 1.0
OE1 C:GLU34 2.1 33.1 1.0
CE1 C:HIS35 3.0 30.2 1.0
CG C:HIS35 3.1 30.1 1.0
CD C:GLU34 3.2 60.3 1.0
CB C:HIS35 3.5 29.9 1.0
OE2 C:GLU34 3.5 55.4 1.0
CA C:HIS35 3.6 30.5 1.0
N C:HIS35 4.0 30.9 1.0
NE2 C:HIS35 4.1 29.4 1.0
CD2 C:HIS35 4.2 29.7 1.0
C C:GLU34 4.4 33.8 1.0
CG C:GLU34 4.5 41.3 1.0
O C:HOH220 4.5 45.5 1.0
O C:GLU31 4.6 34.6 1.0
O C:GLU34 4.6 34.7 1.0
CB C:GLU34 4.8 31.8 1.0
C C:HIS35 4.9 42.7 1.0

Reference:

L.Ruckthong, J.A.Stuckey, V.L.Pecoraro. How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation. Chemistry V. 25 6773 2019.
ISSN: ISSN 0947-6539
PubMed: 30861211
DOI: 10.1002/CHEM.201806040
Page generated: Wed Dec 16 11:42:59 2020

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