Zinc in PDB 7eyi: Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation

Protein crystallography data

The structure of Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation, PDB code: 7eyi was solved by Y.Yang, Y.Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.72 / 2.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.44, 67.44, 228.705, 90, 90, 90
R / Rfree (%) 22.2 / 26.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation (pdb code 7eyi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation, PDB code: 7eyi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7eyi

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Zinc binding site 1 out of 8 in the Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation


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 ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn601

b:28.0
occ:1.00
NE2 G:HIS404 2.1 31.4 1.0
NE2 G:HIS400 2.1 32.0 1.0
SG G:CYS387 2.3 36.4 1.0
SG G:CYS384 2.4 27.1 1.0
CD2 G:HIS404 2.8 29.0 1.0
CB G:CYS387 2.9 31.8 1.0
CE1 G:HIS400 2.9 30.9 1.0
CB G:CYS384 3.1 20.1 1.0
CD2 G:HIS400 3.1 28.3 1.0
CE1 G:HIS404 3.2 29.8 1.0
N G:CYS387 3.4 29.9 1.0
CA G:CYS387 3.7 29.8 1.0
ND1 G:HIS400 4.1 28.6 1.0
CG G:HIS404 4.1 31.8 1.0
CG G:HIS400 4.2 30.1 1.0
ND1 G:HIS404 4.2 34.5 1.0
CB G:ILE386 4.5 28.1 1.0
C G:ILE386 4.5 31.6 1.0
C G:CYS387 4.6 28.5 1.0
CA G:CYS384 4.6 27.9 1.0
N G:GLU388 4.7 31.7 1.0
CA G:ILE386 4.9 26.5 1.0
N G:ILE386 4.9 26.3 1.0

Zinc binding site 2 out of 8 in 7eyi

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Zinc binding site 2 out of 8 in the Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation


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 ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn602

b:40.1
occ:1.00
NE2 G:HIS428 2.1 43.0 1.0
NE2 G:HIS432 2.2 50.9 1.0
SG G:CYS415 2.3 53.8 1.0
SG G:CYS412 2.3 37.2 1.0
CD2 G:HIS432 2.8 43.6 1.0
CD2 G:HIS428 2.9 38.4 1.0
CE1 G:HIS428 3.2 38.9 1.0
CB G:CYS412 3.3 52.8 1.0
CB G:CYS415 3.3 49.0 1.0
CE1 G:HIS432 3.4 45.6 1.0
N G:CYS415 3.6 52.0 1.0
CA G:CYS415 4.0 51.3 1.0
CG G:HIS432 4.0 42.8 1.0
CG G:HIS428 4.1 37.0 1.0
ND1 G:HIS428 4.2 39.9 1.0
ND1 G:HIS432 4.2 45.5 1.0
CB G:ILE414 4.5 44.2 1.0
SD G:MET429 4.6 58.8 1.0
C G:ILE414 4.7 53.9 1.0
C G:CYS415 4.7 55.7 1.0
CA G:CYS412 4.7 50.2 1.0
N G:LYS416 4.7 57.5 1.0
N G:ILE414 4.9 53.9 1.0
CA G:ILE414 4.9 49.5 1.0

Zinc binding site 3 out of 8 in 7eyi

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Zinc binding site 3 out of 8 in the Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation


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 ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn603

b:36.2
occ:1.00
NE2 G:HIS460 2.0 41.8 1.0
NE2 G:HIS456 2.2 46.7 1.0
SG G:CYS440 2.3 36.8 1.0
SG G:CYS443 2.4 36.3 1.0
CD2 G:HIS456 2.8 39.5 1.0
CE1 G:HIS460 3.0 35.9 1.0
CD2 G:HIS460 3.0 36.2 1.0
CB G:CYS443 3.2 34.1 1.0
CB G:CYS440 3.3 37.7 1.0
CE1 G:HIS456 3.3 41.8 1.0
N G:CYS443 3.5 40.7 1.0
CA G:CYS443 3.9 40.2 1.0
CG G:HIS456 4.1 40.4 1.0
ND1 G:HIS460 4.1 36.7 1.0
CG G:HIS460 4.2 38.6 1.0
ND1 G:HIS456 4.3 42.1 1.0
CE G:MET457 4.3 44.4 1.0
CB G:GLN442 4.3 41.7 1.0
C G:GLN442 4.6 38.7 1.0
CA G:CYS440 4.7 38.1 1.0
C G:CYS443 4.7 42.2 1.0
N G:GLN442 4.8 42.8 1.0
N G:GLY444 4.8 39.0 1.0
CA G:GLN442 4.8 39.8 1.0
CB G:ALA445 4.9 25.8 1.0

Zinc binding site 4 out of 8 in 7eyi

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Zinc binding site 4 out of 8 in the Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation


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 ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn604

b:79.7
occ:1.00
CB G:CYS471 2.1 75.5 1.0
NE2 G:HIS484 2.2 67.2 1.0
SG G:CYS468 2.5 57.3 1.0
SG G:CYS490 2.6 79.1 1.0
CE1 G:HIS484 2.9 67.7 1.0
SG G:CYS471 2.9 74.8 1.0
CA G:CYS471 3.0 75.8 1.0
N G:CYS471 3.2 79.9 1.0
CD2 G:HIS484 3.3 62.6 1.0
CB G:CYS468 3.3 51.5 1.0
ND1 G:HIS484 4.0 64.2 1.0
CB G:CYS490 4.1 82.7 1.0
C G:CYS471 4.1 70.9 1.0
OG G:SER470 4.2 81.7 1.0
CG G:HIS484 4.3 60.2 1.0
C G:SER470 4.3 85.2 1.0
N G:CYS472 4.5 68.5 1.0
O G:CYS468 4.6 62.2 1.0
CA G:CYS468 4.7 54.7 1.0
CB G:LYS473 4.8 54.1 1.0
CB G:SER470 4.9 79.4 1.0
O G:CYS471 4.9 70.7 1.0
N G:LYS473 4.9 57.5 1.0
CA G:SER470 4.9 81.3 1.0
C G:CYS468 5.0 60.7 1.0

Zinc binding site 5 out of 8 in 7eyi

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Zinc binding site 5 out of 8 in the Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation


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 ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn601

b:32.3
occ:1.00
NE2 H:HIS432 2.1 38.3 1.0
NE2 H:HIS428 2.2 31.6 1.0
SG H:CYS415 2.3 31.0 1.0
SG H:CYS412 2.3 29.3 1.0
CD2 H:HIS428 2.9 27.1 1.0
CD2 H:HIS432 3.0 34.2 1.0
CE1 H:HIS432 3.2 33.8 1.0
CB H:CYS412 3.2 32.2 1.0
CB H:CYS415 3.3 28.2 1.0
CE1 H:HIS428 3.3 32.2 1.0
N H:CYS415 3.7 40.0 1.0
CA H:CYS415 4.1 38.0 1.0
CG H:HIS428 4.2 24.5 1.0
CG H:HIS432 4.2 32.5 1.0
ND1 H:HIS432 4.3 35.6 1.0
ND1 H:HIS428 4.3 28.4 1.0
CE H:MET429 4.4 29.3 1.0
CB H:ILE414 4.4 31.0 1.0
CA H:CYS412 4.7 31.2 1.0
C H:ILE414 4.8 38.3 1.0
C H:CYS415 4.9 40.4 1.0

Zinc binding site 6 out of 8 in 7eyi

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Zinc binding site 6 out of 8 in the Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation


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 ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn602

b:42.4
occ:1.00
NE2 H:HIS456 2.1 56.1 1.0
NE2 H:HIS460 2.2 70.3 1.0
SG H:CYS443 2.3 51.7 1.0
CD2 H:HIS460 2.4 65.2 1.0
SG H:CYS440 2.6 48.4 1.0
CE1 H:HIS456 2.8 53.1 1.0
CB H:CYS443 2.8 44.2 1.0
CD2 H:HIS456 3.3 50.1 1.0
CE1 H:HIS460 3.4 71.2 1.0
CB H:CYS440 3.4 39.6 1.0
N H:CYS443 3.4 47.3 1.0
CG H:HIS460 3.6 66.8 1.0
CA H:CYS443 3.7 46.7 1.0
ND1 H:HIS456 4.0 51.0 1.0
ND1 H:HIS460 4.0 71.1 1.0
CG H:HIS456 4.2 47.6 1.0
CB H:GLN442 4.6 52.7 1.0
C H:GLN442 4.6 51.2 1.0
C H:CYS443 4.6 46.1 1.0
N H:GLY444 4.7 43.5 1.0
CB H:HIS460 4.7 66.1 1.0
SD H:MET457 4.8 55.1 1.0
CA H:CYS440 4.9 41.8 1.0
CA H:GLN442 5.0 51.0 1.0

Zinc binding site 7 out of 8 in 7eyi

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Zinc binding site 7 out of 8 in the Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation


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 ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn603

b:24.0
occ:1.00
NE2 H:HIS400 2.1 27.2 1.0
NE2 H:HIS404 2.2 28.0 1.0
SG H:CYS387 2.4 30.6 1.0
SG H:CYS384 2.4 26.6 1.0
CD2 H:HIS400 3.0 25.3 1.0
CD2 H:HIS404 3.0 26.9 1.0
CB H:CYS384 3.1 22.1 1.0
CE1 H:HIS400 3.1 24.1 1.0
CB H:CYS387 3.2 29.8 1.0
CE1 H:HIS404 3.2 29.3 1.0
N H:CYS387 3.6 31.8 1.0
CA H:CYS387 3.9 31.9 1.0
CG H:HIS400 4.1 22.8 1.0
ND1 H:HIS400 4.2 21.9 1.0
CG H:HIS404 4.2 27.9 1.0
ND1 H:HIS404 4.3 28.2 1.0
CB H:ILE386 4.5 26.4 1.0
CA H:CYS384 4.6 32.9 1.0
C H:CYS387 4.6 32.4 1.0
C H:ILE386 4.6 31.5 1.0
N H:GLU388 4.8 34.0 1.0
N H:ILE386 4.9 25.6 1.0
CA H:ILE386 4.9 28.9 1.0

Zinc binding site 8 out of 8 in 7eyi

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Zinc binding site 8 out of 8 in the Crystal Structure of ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation


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 ZBTB7A in Complex with Gamma-Globin -200 Sequence Element with C-194A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn604

b:107.1
occ:1.00
CB H:CYS471 2.4 121.9 1.0
SG H:CYS490 2.5 134.0 1.0
NE2 H:HIS484 2.6 88.5 1.0
SG H:CYS468 3.0 93.1 1.0
CD2 H:HIS484 3.1 83.8 1.0
SG H:CYS471 3.2 123.7 1.0
CA H:CYS471 3.5 124.3 1.0
N H:CYS471 3.6 117.8 1.0
CE1 H:HIS484 3.8 88.1 1.0
C H:SER470 3.9 114.9 1.0
CB H:CYS468 4.0 91.6 1.0
CB H:CYS490 4.1 141.2 1.0
O H:SER470 4.1 116.1 1.0
CG H:HIS484 4.4 81.0 1.0
OG H:SER470 4.4 105.4 1.0
CB H:SER470 4.5 105.4 1.0
CD2 H:LEU485 4.7 70.5 1.0
CA H:SER470 4.7 107.8 1.0
ND1 H:HIS484 4.7 84.1 1.0
C H:CYS471 4.8 125.5 1.0
N H:SER470 5.0 101.2 1.0

Reference:

Y.Yang, R.Ren, L.Ly, J.Horton, F.Li, K.Quinlan, M.Crossley, Y.Y.Shi, X.Cheng. Structural Basis For Human ZBTB7A Action at the Fetal Globin Promoter. Cell Rep 2021.
ISSN: ESSN 2211-1247
Page generated: Fri Sep 24 17:05:39 2021

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