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Zinc in PDB 1mey: Crystal Structure of A Designed Zinc Finger Protein Bound to Dna

Protein crystallography data

The structure of Crystal Structure of A Designed Zinc Finger Protein Bound to Dna, PDB code: 1mey was solved by C.A.Kim, J.M.Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.070, 165.530, 46.274, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 31.9

Other elements in 1mey:

The structure of Crystal Structure of A Designed Zinc Finger Protein Bound to Dna also contains other interesting chemical elements:

Iodine (I) 2 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Designed Zinc Finger Protein Bound to Dna (pdb code 1mey). 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 A Designed Zinc Finger Protein Bound to Dna, PDB code: 1mey:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1mey

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Zinc binding site 1 out of 8 in the Crystal Structure of A Designed Zinc Finger Protein Bound to Dna


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 Designed Zinc Finger Protein Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn88

b:35.3
occ:1.00
 NE2 C:HIS27 2.0 18.0 1.0
NE2 C:HIS23 2.0 20.1 1.0
SG C:CYS10 2.1 27.6 1.0
SG C:CYS7 2.3 25.6 1.0
CD2 C:HIS23 3.0 16.4 1.0
CE1 C:HIS27 3.0 17.6 1.0
CD2 C:HIS27 3.0 11.7 1.0
CE1 C:HIS23 3.1 10.8 1.0
CB C:CYS10 3.1 25.1 1.0
CB C:CYS7 3.3 27.8 1.0
N C:CYS10 3.5 24.3 1.0
CA C:CYS10 3.8 21.5 1.0
ND1 C:HIS27 4.2 17.9 1.0
CG C:HIS23 4.2 15.0 1.0
CG C:HIS27 4.2 16.4 1.0
CB C:GLU9 4.2 32.2 1.0
ND1 C:HIS23 4.2 16.9 1.0
C C:GLU9 4.3 26.4 1.0
O C:HOH118 4.4 18.3 1.0
C C:CYS10 4.6 19.4 1.0
CA C:GLU9 4.7 29.2 1.0
CA C:CYS7 4.7 27.8 1.0
N C:GLY11 4.7 15.6 1.0
N C:GLU9 4.9 29.9 1.0
N C:LYS12 5.0 18.6 1.0

Zinc binding site 2 out of 8 in 1mey

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Zinc binding site 2 out of 8 in the Crystal Structure of A Designed Zinc Finger Protein Bound to Dna


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 Designed Zinc Finger Protein Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn89

b:23.0
occ:1.00
 NE2 C:HIS51 2.0 14.8 1.0
NE2 C:HIS55 2.0 17.0 1.0
SG C:CYS35 2.2 19.4 1.0
SG C:CYS38 2.3 27.0 1.0
CD2 C:HIS55 3.0 16.5 1.0
CD2 C:HIS51 3.0 15.6 1.0
CE1 C:HIS51 3.0 9.1 1.0
CE1 C:HIS55 3.1 12.1 1.0
CB C:CYS35 3.2 21.8 1.0
CB C:CYS38 3.4 24.8 1.0
N C:CYS38 3.5 27.7 1.0
CA C:CYS38 4.0 28.0 1.0
ND1 C:HIS51 4.2 8.4 1.0
CG C:HIS55 4.2 16.1 1.0
CG C:HIS51 4.2 10.3 1.0
ND1 C:HIS55 4.2 16.6 1.0
CB C:GLU37 4.6 21.8 1.0
C C:GLU37 4.6 26.4 1.0
CA C:CYS35 4.6 22.7 1.0
N C:GLY39 4.7 28.2 1.0
C C:CYS38 4.7 28.4 1.0
CA C:GLU37 4.9 24.0 1.0
CB C:LYS40 4.9 26.2 1.0
CG C:GLU37 4.9 21.2 1.0
N C:LYS40 4.9 26.4 1.0
N C:GLU37 5.0 25.9 1.0

Zinc binding site 3 out of 8 in 1mey

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Zinc binding site 3 out of 8 in the Crystal Structure of A Designed Zinc Finger Protein Bound to Dna


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 Designed Zinc Finger Protein Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn90

b:39.8
occ:1.00
 NE2 C:HIS83 1.8 32.6 1.0
NE2 C:HIS79 2.1 35.4 1.0
SG C:CYS63 2.2 29.2 1.0
SG C:CYS66 2.3 33.2 1.0
CE1 C:HIS83 2.8 33.3 1.0
CD2 C:HIS83 2.9 35.2 1.0
CE1 C:HIS79 3.1 32.8 1.0
CD2 C:HIS79 3.1 31.6 1.0
CB C:CYS63 3.3 30.6 1.0
CB C:CYS66 3.7 33.1 1.0
N C:CYS66 3.7 36.4 1.0
ND1 C:HIS83 3.9 36.4 1.0
CG C:HIS83 4.0 34.9 1.0
CA C:CYS66 4.2 33.3 1.0
CB C:GLU65 4.3 43.7 1.0
ND1 C:HIS79 4.3 32.7 1.0
CG C:HIS79 4.3 29.4 1.0
C C:GLU65 4.5 39.2 1.0
N C:GLU65 4.7 39.4 1.0
CA C:GLU65 4.7 40.1 1.0
CA C:CYS63 4.7 33.0 1.0
C C:CYS66 5.0 32.8 1.0

Zinc binding site 4 out of 8 in 1mey

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Zinc binding site 4 out of 8 in the Crystal Structure of A Designed Zinc Finger Protein Bound to Dna


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 A Designed Zinc Finger Protein Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn88

b:55.0
occ:1.00
 NE2 F:HIS23 2.0 43.3 1.0
NE2 F:HIS27 2.0 52.4 1.0
SG F:CYS10 2.3 46.0 1.0
SG F:CYS7 2.5 47.8 1.0
CB F:CYS10 2.9 46.1 1.0
CD2 F:HIS27 3.0 54.9 1.0
CE1 F:HIS23 3.0 38.0 1.0
CD2 F:HIS23 3.0 39.0 1.0
CE1 F:HIS27 3.1 57.0 1.0
N F:CYS10 3.4 49.3 1.0
CB F:CYS7 3.4 50.9 1.0
CA F:CYS10 3.7 47.3 1.0
C F:GLU9 4.1 50.2 1.0
ND1 F:HIS23 4.1 37.7 1.0
CG F:HIS23 4.2 35.1 1.0
CG F:HIS27 4.2 54.8 1.0
N F:GLY11 4.2 47.3 1.0
ND1 F:HIS27 4.2 57.0 1.0
C F:CYS10 4.5 46.7 1.0
CA F:GLU9 4.7 50.4 1.0
N F:LYS12 4.7 41.6 1.0
CB F:LYS12 4.7 38.5 1.0
N F:GLU9 4.7 49.6 1.0
O D:HOH14 4.8 35.8 1.0
CB F:GLU9 4.8 51.7 1.0
O F:GLU9 4.8 51.6 1.0
CA F:CYS7 4.8 49.9 1.0

Zinc binding site 5 out of 8 in 1mey

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Zinc binding site 5 out of 8 in the Crystal Structure of A Designed Zinc Finger Protein Bound to Dna


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 A Designed Zinc Finger Protein Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn89

b:65.8
occ:1.00
 NE2 F:HIS55 1.9 56.4 1.0
NE2 F:HIS51 2.0 55.6 1.0
SG F:CYS38 2.3 56.4 1.0
SG F:CYS35 2.3 60.4 1.0
CD2 F:HIS55 2.9 56.4 1.0
CE1 F:HIS55 2.9 56.6 1.0
CD2 F:HIS51 3.0 54.7 1.0
CE1 F:HIS51 3.1 47.8 1.0
N F:CYS38 3.3 55.1 1.0
CB F:CYS35 3.3 55.6 1.0
CB F:CYS38 3.4 54.4 1.0
CB F:GLU37 3.8 55.6 1.0
CA F:CYS38 3.9 54.8 1.0
ND1 F:HIS55 4.0 56.2 1.0
CG F:HIS55 4.0 58.6 1.0
CG F:HIS51 4.2 52.8 1.0
ND1 F:HIS51 4.2 51.6 1.0
C F:GLU37 4.3 55.0 1.0
N F:GLY39 4.4 52.2 1.0
CB F:LYS40 4.4 55.2 1.0
CA F:GLU37 4.5 54.6 1.0
C F:CYS38 4.6 53.3 1.0
N F:GLU37 4.7 53.8 1.0
N F:LYS40 4.8 54.3 1.0
CG F:GLU37 4.8 58.9 1.0
CA F:CYS35 4.8 54.1 1.0

Zinc binding site 6 out of 8 in 1mey

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Zinc binding site 6 out of 8 in the Crystal Structure of A Designed Zinc Finger Protein Bound to Dna


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 A Designed Zinc Finger Protein Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn90

b:66.3
occ:1.00
 NE2 F:HIS83 1.8 52.9 1.0
NE2 F:HIS79 2.0 58.1 1.0
SG F:CYS66 2.3 52.6 1.0
SG F:CYS63 2.4 57.0 1.0
CE1 F:HIS83 2.8 48.5 1.0
CD2 F:HIS83 2.9 48.1 1.0
CD2 F:HIS79 3.0 56.3 1.0
CE1 F:HIS79 3.1 55.4 1.0
CB F:CYS63 3.2 57.5 1.0
CB F:CYS66 3.3 50.5 1.0
N F:CYS66 3.5 47.9 1.0
CA F:CYS66 3.9 49.0 1.0
ND1 F:HIS83 4.0 49.2 1.0
CG F:HIS83 4.0 48.8 1.0
CG F:HIS79 4.2 52.7 1.0
ND1 F:HIS79 4.2 54.6 1.0
CB F:GLU65 4.3 50.0 1.0
CB F:LYS68 4.3 49.1 1.0
C F:GLU65 4.6 48.0 1.0
C F:CYS66 4.7 48.0 1.0
CA F:CYS63 4.7 55.7 1.0
N F:GLY67 4.8 47.9 1.0
CA F:GLU65 4.8 48.3 1.0
CG F:GLN80 4.9 65.9 1.0
CG F:LYS68 4.9 45.4 1.0
N F:LYS68 4.9 50.9 1.0
N F:GLU65 5.0 49.0 1.0

Zinc binding site 7 out of 8 in 1mey

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Zinc binding site 7 out of 8 in the Crystal Structure of A Designed Zinc Finger Protein Bound to Dna


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 A Designed Zinc Finger Protein Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn90

b:30.2
occ:1.00
 NE2 G:HIS83 2.0 20.2 1.0
NE2 G:HIS79 2.0 22.8 1.0
SG G:CYS63 2.3 19.5 1.0
SG G:CYS66 2.3 21.8 1.0
CE1 G:HIS83 2.9 19.5 1.0
CD2 G:HIS83 3.0 22.8 1.0
CE1 G:HIS79 3.0 21.3 1.0
CD2 G:HIS79 3.1 20.9 1.0
CB G:CYS63 3.1 24.7 1.0
CB G:CYS66 3.4 19.3 1.0
N G:CYS66 3.5 22.3 1.0
CA G:CYS66 4.0 16.4 1.0
CB G:GLU65 4.1 29.2 1.0
ND1 G:HIS83 4.1 19.0 1.0
CG G:HIS83 4.1 20.2 1.0
ND1 G:HIS79 4.2 21.2 1.0
CG G:HIS79 4.2 21.4 1.0
C G:GLU65 4.4 26.0 1.0
CB G:LYS68 4.5 17.7 1.0
CA G:CYS63 4.6 26.1 1.0
CA G:GLU65 4.6 25.8 1.0
N G:GLU65 4.7 25.2 1.0
C G:CYS66 4.7 17.1 1.0
N G:GLY67 4.9 17.6 1.0

Zinc binding site 8 out of 8 in 1mey

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Zinc binding site 8 out of 8 in the Crystal Structure of A Designed Zinc Finger Protein Bound to Dna


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 A Designed Zinc Finger Protein Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn91

b:27.1
occ:1.00
 O C:HOH110 1.8 32.2 1.0
CL G:CL92 2.0 30.8 1.0
ND1 G:HIS75 2.0 19.2 1.0
ND1 C:HIS27 2.2 17.9 1.0
CE1 C:HIS27 2.9 17.6 1.0
CG G:HIS75 3.0 18.6 1.0
CE1 G:HIS75 3.0 20.3 1.0
CB G:HIS75 3.3 21.2 1.0
CG C:HIS27 3.4 16.4 1.0
O C:HOH92 3.9 19.3 1.0
CB C:HIS27 3.9 17.0 1.0
CA C:HIS27 4.0 19.6 1.0
O C:HOH140 4.1 26.0 1.0
NE2 G:HIS75 4.1 21.7 1.0
CD2 G:HIS75 4.1 18.8 1.0
NE2 C:HIS27 4.1 18.0 1.0
CD2 C:HIS27 4.4 11.7 1.0
CG G:ARG72 4.4 25.9 1.0
CD1 G:PHE70 4.4 14.2 1.0
CD G:ARG72 4.5 30.1 1.0
OE1 C:GLU9 4.7 49.0 1.0
O G:HOH93 4.7 23.7 1.0
CA G:HIS75 4.8 21.5 1.0
N C:HIS27 4.8 18.4 1.0
O C:THR26 4.8 20.0 1.0
NZ G:LYS59 4.9 41.8 1.0
CE1 G:PHE70 4.9 10.5 1.0

Reference:

C.A.Kim, J.M.Berg. A 2.2 A Resolution Crystal Structure of A Designed Zinc Finger Protein Bound to Dna Nat.Struct.Biol. V. 3 940 1996.
ISSN: ISSN 1072-8368
PubMed: 8901872
DOI: 10.1038/NSB1196-940
Page generated: Wed Dec 16 02:57:03 2020

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