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Cadmium in PDB 4mm2: Crystal Structure of Yeast Primase Catalytic Subunit

Protein crystallography data

The structure of Crystal Structure of Yeast Primase Catalytic Subunit, PDB code: 4mm2 was solved by K.R.Park, J.Y.An, Y.Lee, H.S.Youn, J.G.Lee, J.Y.Kang, T.G.Kim, J.J.Lim, S.H.Eom, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.88 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.370, 196.040, 53.960, 90.00, 114.72, 90.00
R / Rfree (%) 25.5 / 29.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Yeast Primase Catalytic Subunit (pdb code 4mm2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Crystal Structure of Yeast Primase Catalytic Subunit, PDB code: 4mm2:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 4mm2

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Cadmium binding site 1 out of 10 in the Crystal Structure of Yeast Primase Catalytic Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Yeast Primase Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:18.0
occ:1.00
 SG A:CYS124 2.2 12.0 1.0
SG A:CYS123 2.5 20.7 1.0
SG A:CYS133 2.5 15.9 1.0
SG A:CYS130 2.5 19.6 1.0
CB A:CYS133 3.4 21.3 1.0
CB A:CYS123 3.5 17.1 1.0
CB A:CYS124 3.5 16.1 1.0
N A:CYS130 3.5 18.9 1.0
N A:CYS124 3.6 19.5 1.0
CB A:CYS130 3.6 20.0 1.0
C A:CYS123 3.7 21.5 1.0
N A:CYS133 3.8 17.1 1.0
CA A:CYS130 4.0 18.9 1.0
CD A:CD504 4.1 20.5 1.0
O A:CYS123 4.1 23.7 1.0
CA A:CYS124 4.1 22.6 1.0
C A:VAL129 4.1 19.0 1.0
CA A:CYS123 4.2 21.8 1.0
CA A:CYS133 4.2 22.9 1.0
CD A:CD505 4.3 58.2 1.0
O A:CYS130 4.4 15.4 1.0
CA A:VAL129 4.5 13.5 1.0
C A:CYS130 4.5 16.6 1.0
CB A:LYS132 4.6 22.9 1.0
NH1 A:ARG121 4.8 17.1 1.0
C A:LYS132 4.9 21.0 1.0
O A:VAL129 4.9 18.7 1.0
N A:CYS123 4.9 18.2 1.0

Cadmium binding site 2 out of 10 in 4mm2

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Cadmium binding site 2 out of 10 in the Crystal Structure of Yeast Primase Catalytic Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Yeast Primase Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:15.8
occ:1.00
 O A:HOH646 2.3 8.9 1.0
OD1 A:ASP111 2.4 9.3 1.0
OD1 A:ASP113 2.5 14.4 1.0
NE2 A:HIS168 2.6 16.2 1.0
O A:HOH633 2.7 17.3 1.0
O4 A:CIT506 3.0 8.9 1.0
CG A:ASP111 3.1 10.6 1.0
OD2 A:ASP111 3.2 7.2 1.0
CD2 A:HIS168 3.4 14.8 1.0
CG A:ASP113 3.5 15.3 1.0
CD A:CD503 3.5 18.1 1.0
C4 A:CIT506 3.6 18.9 1.0
C5 A:CIT506 3.7 16.7 1.0
CE1 A:HIS168 3.7 15.2 1.0
OD2 A:ASP113 3.9 18.1 1.0
CB A:SER162 4.4 11.0 1.0
O A:ILE112 4.4 14.1 1.0
CB A:ASP111 4.6 12.1 1.0
CG A:HIS168 4.7 13.8 1.0
OG A:SER162 4.7 15.2 1.0
CB A:ASP113 4.7 11.6 1.0
C A:ILE112 4.8 14.5 1.0
ND1 A:HIS168 4.8 14.2 1.0
O3 A:CIT506 4.9 26.4 1.0
CA A:ASP113 4.9 11.6 1.0
N A:ASP113 4.9 13.7 1.0
NH1 A:ARG165 5.0 13.5 1.0

Cadmium binding site 3 out of 10 in 4mm2

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Cadmium binding site 3 out of 10 in the Crystal Structure of Yeast Primase Catalytic Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Yeast Primase Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:18.1
occ:1.00
 OD2 A:ASP113 2.2 18.1 1.0
OD2 A:ASP314 2.4 8.2 0.5
OD2 A:ASP111 2.4 7.2 1.0
OD2 A:ASP314 2.6 16.1 0.5
CG A:ASP113 3.2 15.3 1.0
CG A:ASP314 3.2 11.7 0.5
CG A:ASP111 3.4 10.6 1.0
OD1 A:ASP113 3.4 14.4 1.0
CG A:ASP314 3.5 25.1 0.5
CD A:CD502 3.5 15.8 1.0
CB A:ASP314 3.5 15.6 0.5
CB A:ASP314 3.6 23.1 0.5
OD1 A:ASP111 3.8 9.3 1.0
O A:HOH726 4.0 29.8 1.0
O A:HOH659 4.0 19.9 1.0
O A:HOH633 4.0 17.3 1.0
OD1 A:ASP314 4.2 10.0 0.5
CG2 A:VAL317 4.5 18.2 0.5
NH1 A:ARG165 4.5 13.5 1.0
CB A:ASP113 4.5 11.6 1.0
CG1 A:VAL317 4.6 11.6 0.5
CB A:ASP111 4.6 12.1 1.0
O A:HOH695 4.6 28.6 1.0
OD1 A:ASP314 4.7 29.9 0.5
O A:HOH651 4.7 23.8 1.0
NH2 A:ARG165 5.0 16.5 1.0

Cadmium binding site 4 out of 10 in 4mm2

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Cadmium binding site 4 out of 10 in the Crystal Structure of Yeast Primase Catalytic Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Yeast Primase Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd504

b:20.5
occ:1.00
 O A:CYS123 2.3 23.7 1.0
SG A:CYS124 2.7 12.0 1.0
C A:CYS123 3.3 21.5 1.0
CB A:CYS124 3.5 16.1 1.0
CA A:CYS124 3.7 22.6 1.0
N A:CYS124 3.8 19.5 1.0
CD A:CD501 4.1 18.0 1.0
CD A:CD505 4.2 58.2 1.0
CG A:GLN128 4.4 31.3 1.0
CA A:CYS123 4.5 21.8 1.0
SG A:CYS130 4.6 19.6 1.0
CB A:CYS123 4.7 17.1 1.0
NE2 A:GLN128 4.9 32.8 1.0
CB A:CYS130 4.9 20.0 1.0
O A:HOH634 5.0 20.7 1.0

Cadmium binding site 5 out of 10 in 4mm2

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Cadmium binding site 5 out of 10 in the Crystal Structure of Yeast Primase Catalytic Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Yeast Primase Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd505

b:58.2
occ:1.00
 SG A:CYS130 2.5 19.6 1.0
CB A:CYS130 3.4 20.0 1.0
CD A:LYS132 4.0 33.1 1.0
CG A:LYS132 4.1 29.8 1.0
CD A:CD504 4.2 20.5 1.0
CD A:CD501 4.3 18.0 1.0
CB A:CYS123 4.5 17.1 1.0
O A:HOH722 4.5 24.1 1.0
CB A:LYS132 4.6 22.9 1.0
CA A:CYS130 4.9 18.9 1.0
O A:CYS123 4.9 23.7 1.0
SG A:CYS124 4.9 12.0 1.0
SG A:CYS123 5.0 20.7 1.0

Cadmium binding site 6 out of 10 in 4mm2

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Cadmium binding site 6 out of 10 in the Crystal Structure of Yeast Primase Catalytic Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Yeast Primase Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd501

b:21.1
occ:1.00
 SG B:CYS124 2.2 20.7 1.0
SG B:CYS133 2.4 22.2 1.0
SG B:CYS123 2.5 21.9 1.0
SG B:CYS130 2.5 20.2 1.0
CB B:CYS133 3.4 28.0 1.0
CB B:CYS124 3.5 14.0 1.0
CB B:CYS123 3.5 20.2 1.0
N B:CYS130 3.5 24.8 1.0
N B:CYS124 3.6 24.6 1.0
CB B:CYS130 3.6 19.0 1.0
C B:CYS123 3.8 24.3 1.0
N B:CYS133 3.8 27.8 1.0
CA B:CYS130 4.0 22.8 1.0
CD B:CD504 4.1 23.3 1.0
CA B:CYS124 4.1 23.9 1.0
O B:CYS123 4.1 27.9 1.0
C B:VAL129 4.1 28.1 1.0
CA B:CYS133 4.2 26.7 1.0
CA B:CYS123 4.2 20.4 1.0
O B:CYS130 4.4 24.2 1.0
CD B:CD505 4.4 67.5 1.0
C B:CYS130 4.5 19.5 1.0
CA B:VAL129 4.5 28.3 1.0
NH2 B:ARG121 4.5 19.5 1.0
CB B:LYS132 4.7 24.7 1.0
C B:LYS132 4.9 24.5 1.0
O B:VAL129 4.9 27.3 1.0
N B:CYS123 5.0 20.4 1.0

Cadmium binding site 7 out of 10 in 4mm2

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Cadmium binding site 7 out of 10 in the Crystal Structure of Yeast Primase Catalytic Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Yeast Primase Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd502

b:23.5
occ:1.00
 OD1 B:ASP111 2.4 13.9 1.0
OD1 B:ASP113 2.4 13.3 1.0
O4 B:CIT506 2.5 16.6 1.0
NE2 B:HIS168 2.8 12.3 1.0
CG B:ASP111 3.1 18.7 1.0
O B:HOH645 3.2 34.3 1.0
OD2 B:ASP111 3.2 10.6 1.0
C4 B:CIT506 3.3 29.5 1.0
C5 B:CIT506 3.3 37.9 1.0
CG B:ASP113 3.4 11.2 1.0
CD B:CD503 3.5 25.6 1.0
CD2 B:HIS168 3.5 11.2 1.0
OD2 B:ASP113 3.8 12.3 1.0
CE1 B:HIS168 3.8 19.1 1.0
CB B:SER162 4.3 16.5 1.0
O B:ILE112 4.4 11.6 1.0
O B:HOH683 4.4 32.2 1.0
O3 B:CIT506 4.5 24.5 1.0
O B:HOH790 4.5 34.0 1.0
CB B:ASP111 4.6 12.6 1.0
OG B:SER162 4.6 20.9 1.0
CB B:ASP113 4.7 13.2 1.0
C B:ILE112 4.7 11.3 1.0
NH1 B:ARG165 4.7 23.3 1.0
CG B:HIS168 4.8 13.6 1.0
C3 B:CIT506 4.8 34.2 1.0
O7 B:CIT506 4.9 37.2 1.0
CA B:ASP113 4.9 15.9 1.0
ND1 B:HIS168 4.9 18.6 1.0
N B:ASP113 4.9 14.2 1.0
N B:ILE112 4.9 13.2 1.0

Cadmium binding site 8 out of 10 in 4mm2

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Cadmium binding site 8 out of 10 in the Crystal Structure of Yeast Primase Catalytic Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Yeast Primase Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd503

b:25.6
occ:1.00
 OD2 B:ASP113 2.2 12.3 1.0
OD2 B:ASP111 2.4 10.6 1.0
OD2 B:ASP314 2.8 19.8 1.0
CG B:ASP113 3.2 11.2 1.0
CG B:ASP111 3.3 18.7 1.0
CG B:ASP314 3.4 25.6 1.0
OD1 B:ASP113 3.4 13.3 1.0
CD B:CD502 3.5 23.5 1.0
CB B:ASP314 3.6 25.2 1.0
OD1 B:ASP111 3.7 13.9 1.0
O B:HOH790 3.7 34.0 1.0
O B:HOH743 3.8 32.4 1.0
O B:HOH684 4.0 24.4 1.0
NH1 B:ARG165 4.2 23.3 1.0
OD1 B:ASP314 4.3 26.5 1.0
CG2 B:VAL317 4.5 18.2 1.0
CB B:ASP111 4.5 12.6 1.0
CB B:ASP113 4.6 13.2 1.0
O B:HOH741 4.7 36.4 1.0
CZ B:ARG165 4.9 25.3 1.0
NH2 B:ARG165 4.9 23.7 1.0

Cadmium binding site 9 out of 10 in 4mm2

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Cadmium binding site 9 out of 10 in the Crystal Structure of Yeast Primase Catalytic Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Yeast Primase Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd504

b:23.3
occ:1.00
 O B:CYS123 2.3 27.9 1.0
O B:HOH805 2.6 39.4 1.0
SG B:CYS124 2.7 20.7 1.0
O B:HOH650 3.0 14.8 1.0
C B:CYS123 3.3 24.3 1.0
CB B:CYS124 3.5 14.0 1.0
CA B:CYS124 3.6 23.9 1.0
N B:CYS124 3.8 24.6 1.0
CD B:CD501 4.1 21.1 1.0
CD B:CD505 4.2 67.5 1.0
CG B:GLN128 4.3 42.8 1.0
CA B:CYS123 4.5 20.4 1.0
SG B:CYS130 4.6 20.2 1.0
CB B:CYS123 4.7 20.2 1.0
NE2 B:GLN128 4.9 56.1 1.0
CB B:CYS130 4.9 19.0 1.0
O B:HOH807 5.0 42.5 1.0

Cadmium binding site 10 out of 10 in 4mm2

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Cadmium binding site 10 out of 10 in the Crystal Structure of Yeast Primase Catalytic Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Yeast Primase Catalytic Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd505

b:67.5
occ:1.00
 O B:HOH807 2.6 42.5 1.0
SG B:CYS130 2.7 20.2 1.0
O B:HOH745 3.2 36.4 1.0
CB B:CYS130 3.5 19.0 1.0
O B:HOH808 3.7 40.0 1.0
CD B:LYS132 4.1 43.6 1.0
O B:HOH650 4.1 14.8 1.0
O B:HOH806 4.1 34.4 1.0
CD B:CD504 4.2 23.3 1.0
CG B:LYS132 4.3 35.2 1.0
O B:HOH805 4.4 39.4 1.0
CD B:CD501 4.4 21.1 1.0
CB B:CYS123 4.5 20.2 1.0
CB B:LYS132 4.8 24.7 1.0
O B:CYS123 4.9 27.9 1.0
CA B:CYS130 5.0 22.8 1.0

Reference:

K.R.Park, J.Y.An, Y.Lee, H.S.Youn, J.G.Lee, J.Y.Kang, T.G.Kim, J.J.Lim, S.H.Eom, J.Wang. Crystal Structure of Yeast Primase Catalytic Subunit To Be Published.
Page generated: Thu Jul 10 13:47:32 2025

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